today <- Sys.Date() # today's date
Mise à jour du 2021-03-10.
Source des données : https://www.data.gouv.fr/fr/datasets/donnees-de-laboratoires-pour-le-depistage-indicateurs-sur-les-variants/
Légende
library("RColorBrewer")
brw <- brewer.pal(12, "Set3")
brw[2] <- brw[12] # Darker yellow
brw[10] <- brw[11] # Lighter shade
colsAge <- c("#000000FF", brw[1:10])
names(colsAge) <- c("0", "9", "19", "29", "39", "49", "59", "69", "79", "89", "90")
pchAge <- c(16, 0:9)
names(pchAge) <- names(colsAge)
cexAge <- c(1.2, rep(1, 10))
names(cexAge) <- names(colsAge)
ages <- c("tous", "0-9", "10-19", "20-29", "30-39", "40-49", "50-59", "60-69", "70-79", "80-89", "90+")
par(mfrow = c(1, 1))
plot(0:1, 0:1, type = "n", axes = FALSE, xlab = "", ylab = "")
legend(x = 0.5, y = 1, legend = ages, pch = pchAge, col = colsAge)
# Données France
URL <- "https://www.data.gouv.fr/fr/datasets/r/c43d7f3f-c9f5-436b-9b26-728f80e0fd52"
dataFile <- paste0("data/France_", today, ".csv") # name file with today's date
download.file(URL, dataFile) # download file from repo
dat.France <- read.csv(dataFile, sep = ";", stringsAsFactors = FALSE)
# Format date
dat.France$date1 <- as.Date(substring(dat.France$semaine, 1, 10))
dat.France$date2 <- as.Date(substring(dat.France$semaine, 12, 21))
# Rewrite time as days since beginning of the data
dat.France$time <- dat.France$date2 - min(dat.France$date2)
# Compute data on total tests
dat.France$Nb_tests_POS <- dat.France$Nb_tests_PCR_TA_crible / (dat.France$Prc_tests_PCR_TA_crible / 100)
# Dictionnary to reformat age class
dic.age <- (0:9)*10 + 4.5 # Median of age classes
names(dic.age) <- as.character(c(0 + (0:8)*10 + 9, 90))
Compare the data to another source – number of positive tests
# Compare to another source
URL <- "https://www.data.gouv.fr/fr/datasets/r/dd0de5d9-b5a5-4503-930a-7b08dc0adc7c"
dataFile <- paste0("data/tests-France_", today, ".csv") # name file with today's date
download.file(URL, dataFile) # download file from repo
dat.tests <- read.csv(dataFile, sep = ";", stringsAsFactors = FALSE)
URL <- "https://www.data.gouv.fr/fr/datasets/r/c1167c4e-8c89-40f2-adb3-1954f8fedfa7"
dataFile <- paste0("data/tests7j-France_", today, ".csv") # name file with today's date
download.file(URL, dataFile) # download file from repo
dat.tests7j <- read.csv(dataFile, sep = ";", stringsAsFactors = FALSE)
dat.tests7j$date1 <- as.Date(substring(dat.tests7j$semaine_glissante, 1, 10))
dat.tests7j$date2 <- as.Date(substring(dat.tests7j$semaine_glissante, 12, 21))
# P nombre de tests positifs
# T nombre de tests total
dat.tests$date <- as.Date(dat.tests$jour)
dateRange <- range(c(range(dat.France$date1), range(dat.France$date2)))
subdat.tests <- dat.tests[dat.tests$date >= dateRange[1] & dat.tests$date <= dateRange[2],]
# Function to compute a sliding window
sliding.window <- function(v, winwdt = 7, pos = 4, na.rm = TRUE){
# v vector to be averaged/summed
# winwdt width of the window
# pos position of the focal day in the window
# FUN function to apply
n <- length(v)
# Initialize output vector
out <- 0 * v + (-1)
out[1:(pos-1)] <- NA
out[(n + 1 - winwdt + pos) : n] <- NA
for(i in pos : (n - winwdt + pos)){
out[i] <- mean(v[(i - pos + 1):(i + winwdt - pos)], na.rm = na.rm)
}
return(out[1:n])
}
subdat.tests.0 <- subdat.tests[subdat.tests$cl_age90 == 0, ]
dat.France.0 <- dat.France[dat.France$cl_age90 == 0, ]
subdat.tests.0$P.7.1 <- 7 * sliding.window(subdat.tests.0$P, pos = 1)
subdat.tests.0$P.7.4 <- 7 * sliding.window(subdat.tests.0$P, pos = 4)
subdat.tests.0$P.7.7 <- 7 * sliding.window(subdat.tests.0$P, pos = 7)
subdat.tests.0$P.8.8 <- 8 * sliding.window(subdat.tests.0$P, pos = 8, winwdt = 8)
plot(dat.France.0$date2, dat.France.0$Nb_tests, ylim = c(1*10^5, 2*10^5), pch = 16,
xlab = "date", ylab = "nombre de tests")
points(subdat.tests.0$date, subdat.tests.0$P.7.1, ylim = c(0, 5*10^5), col = "red")
points(subdat.tests.0$date, subdat.tests.0$P.7.4, ylim = c(0, 5*10^5), col = "green")
points(subdat.tests.0$date, subdat.tests.0$P.7.7, ylim = c(0, 5*10^5), col = "blue")
points(subdat.tests.0$date, subdat.tests.0$P.8.8, ylim = c(0, 5*10^5), col = "purple")
points(dat.tests7j$date2, dat.tests7j$P, pch = 2)
legend(x = as.Date("2021-02-18"), y = 200000, col = c("black", "red", "green", "blue", "purple", "black"), legend = c("sidep tests", "w7, c1", "w7, c4", "w7, c7", "w8, c8", "sidep 7j-fin"), pch = c(16, rep(1, 4), 2))
Legend notation:
w: width of the window, c: position of the index day.
So the sliding window is on the 7 last days.
The difference (about 15% more positives in the variants dataset) may be due to the variant data being in terms of tests, and the other in terms of people, with duplicates removed.
#plot(dat.France.0$date2, dat.France.0$Nb_tests, ylim = c(1*10^5, 2*10^5), pch = 16,
# xlab = "date", ylab = "comparaison nombre de tests")
#points(subdat.tests.0$date, subdat.tests.0$P.7.7, ylim = c(0, 5*10^5), col = "blue")
#points(subdat.tests.0$date, 1.17*subdat.tests.0$P.7.7, ylim = c(0, 5*10^5), col = "orange")
Format the data further (age class data)
# Data per age class
dat.France.ages <- dat.France[dat.France$cl_age90 != 0,]
# Add new age class code -- median of the age class
dat.France.ages$ageClass <- dic.age[as.character(dat.France.ages$cl_age90)]
# Standardize age class values
dat.France.ages$stdage <- (dat.France.ages$ageClass - mean(dat.France.ages$ageClass))/dat.France.ages$ageClass
# All ages, time
par(las = 1)
plot(dat.France$date2, dat.France$Prc_susp_501Y_V1, ylim = c(0, 100),
col = colsAge[as.character(dat.France$cl_age90)],
pch = pchAge[as.character(dat.France$cl_age90)],
cex = cexAge[as.character(dat.France$cl_age90)],
xlab = "date", ylab = "Proportion V1", axes = FALSE)
axis(1, pos = 0, at = as.Date(unique(dat.France$date2)), labels = format(unique(dat.France$date2), format = "%b %d"))
axis(2)
# Plot dp/(p(1-p)) for each age class
ageClasses <- sort(unique(dat.France$cl_age90))
nAge <- length(ageClasses)
for(iage in unique(dat.France$cl_age90)){
sub <- dat.France[dat.France$cl_age90 == iage, ]
V1 <- sub$Prc_susp_501Y_V1/100
t <- sub$date2
s <- diff(V1) / (V1[-length(V1)]*(1-V1[-length(V1)]))
plot(t[-length(V1)], s, ylim = c(-0.1, 0.1), main = iage)
print(c(iage, mean(s)))
}
Binomial model
# Create new colums with information on number of specific PCR tests
# PCR with V1 result
dat.France.ages$V1 <- dat.France.ages$Nb_susp_501Y_V1
# All other PCRs (considering NAs are non-V1)
dat.France.ages$notV1 <- dat.France.ages$Nb_tests_PCR_TA_crible - dat.France.ages$Nb_susp_501Y_V1
# All other PCRs with a result (removing NAs)
dat.France.ages$notV1.narm <- dat.France.ages$Nb_susp_501Y_V2_3 + dat.France.ages$Nb_susp_ABS
# Check that columns correctly sum
all(dat.France.ages$Nb_susp_501Y_V2_3 + dat.France.ages$Nb_susp_ABS + dat.France.ages$Nb_susp_501Y_V1 + dat.France.ages$Nb_susp_IND - dat.France.ages$Nb_tests_PCR_TA_crible == 0)
## [1] TRUE
# GLM
# Assuming that all IND (indetermine) are non-V1
mdl0 <- glm(cbind(V1, notV1) ~ time * factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl0)
##
## Call:
## glm(formula = cbind(V1, notV1) ~ time * factor(ageClass), family = "binomial",
## data = dat.France.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -3.814 -1.069 0.078 1.077 6.067
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.049088 0.014536 3.377 0.000733 ***
## time 0.042181 0.001451 29.069 < 2e-16 ***
## factor(ageClass)14.5 -0.125984 0.016757 -7.518 5.56e-14 ***
## factor(ageClass)24.5 -0.192926 0.016513 -11.684 < 2e-16 ***
## factor(ageClass)34.5 -0.119481 0.016474 -7.253 4.09e-13 ***
## factor(ageClass)44.5 -0.117069 0.016449 -7.117 1.10e-12 ***
## factor(ageClass)54.5 -0.231182 0.016612 -13.917 < 2e-16 ***
## factor(ageClass)64.5 -0.353565 0.017387 -20.335 < 2e-16 ***
## factor(ageClass)74.5 -0.638756 0.018946 -33.714 < 2e-16 ***
## factor(ageClass)84.5 -0.908481 0.020351 -44.641 < 2e-16 ***
## factor(ageClass)94.5 -1.050222 0.024957 -42.081 < 2e-16 ***
## time:factor(ageClass)14.5 0.007233 0.001674 4.321 1.55e-05 ***
## time:factor(ageClass)24.5 0.011140 0.001649 6.754 1.44e-11 ***
## time:factor(ageClass)34.5 0.006262 0.001649 3.797 0.000146 ***
## time:factor(ageClass)44.5 0.007053 0.001649 4.279 1.88e-05 ***
## time:factor(ageClass)54.5 0.009721 0.001664 5.843 5.11e-09 ***
## time:factor(ageClass)64.5 0.009909 0.001736 5.708 1.14e-08 ***
## time:factor(ageClass)74.5 0.024368 0.001893 12.869 < 2e-16 ***
## time:factor(ageClass)84.5 0.023884 0.002059 11.601 < 2e-16 ***
## time:factor(ageClass)94.5 0.019724 0.002594 7.603 2.90e-14 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 47557.1 on 179 degrees of freedom
## Residual deviance: 531.3 on 160 degrees of freedom
## AIC: 2267
##
## Number of Fisher Scoring iterations: 3
# Without interaction
mdl1 <- glm(cbind(V1, notV1) ~ time + factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl1)
##
## Call:
## glm(formula = cbind(V1, notV1) ~ time + factor(ageClass), family = "binomial",
## data = dat.France.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -6.3209 -1.2307 0.2074 1.1558 7.8383
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.0371071 0.0078627 -4.719 2.37e-06 ***
## time 0.0522049 0.0003046 171.379 < 2e-16 ***
## factor(ageClass)14.5 -0.0638032 0.0085359 -7.475 7.74e-14 ***
## factor(ageClass)24.5 -0.0970938 0.0084020 -11.556 < 2e-16 ***
## factor(ageClass)34.5 -0.0652612 0.0084078 -7.762 8.36e-15 ***
## factor(ageClass)44.5 -0.0559737 0.0083973 -6.666 2.63e-11 ***
## factor(ageClass)54.5 -0.1475708 0.0084601 -17.443 < 2e-16 ***
## factor(ageClass)64.5 -0.2683637 0.0088228 -30.417 < 2e-16 ***
## factor(ageClass)74.5 -0.4283992 0.0095582 -44.820 < 2e-16 ***
## factor(ageClass)84.5 -0.7066547 0.0103922 -67.998 < 2e-16 ***
## factor(ageClass)94.5 -0.8866586 0.0130249 -68.074 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 47557.14 on 179 degrees of freedom
## Residual deviance: 880.71 on 169 degrees of freedom
## AIC: 2598.4
##
## Number of Fisher Scoring iterations: 3
## Likelihood ratio test
anova(mdl1, mdl0, test="Chisq")
## Analysis of Deviance Table
##
## Model 1: cbind(V1, notV1) ~ time + factor(ageClass)
## Model 2: cbind(V1, notV1) ~ time * factor(ageClass)
## Resid. Df Resid. Dev Df Deviance Pr(>Chi)
## 1 169 880.71
## 2 160 531.30 9 349.41 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# Test date effect
mdl2 <- glm(cbind(V1, notV1) ~ time * ageClass, data = dat.France.ages, family = "binomial")
summary(mdl2)
##
## Call:
## glm(formula = cbind(V1, notV1) ~ time * ageClass, family = "binomial",
## data = dat.France.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -12.544 -6.159 -1.694 3.303 12.919
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.712e-01 6.496e-03 26.35 <2e-16 ***
## time 4.309e-02 6.566e-04 65.64 <2e-16 ***
## ageClass -8.865e-03 1.344e-04 -65.98 <2e-16 ***
## time:ageClass 2.204e-04 1.368e-05 16.11 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 47557.1 on 179 degrees of freedom
## Residual deviance: 5714.8 on 176 degrees of freedom
## AIC: 7418.5
##
## Number of Fisher Scoring iterations: 3
## Likelihood ratio test
anova(mdl2, mdl0, test="Chisq")
## Analysis of Deviance Table
##
## Model 1: cbind(V1, notV1) ~ time * ageClass
## Model 2: cbind(V1, notV1) ~ time * factor(ageClass)
## Resid. Df Resid. Dev Df Deviance Pr(>Chi)
## 1 176 5714.8
## 2 160 531.3 16 5183.5 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# GLM
# Assuming that all IND (indetermine) are non-V1
mdl0.narm <- glm(cbind(V1, notV1.narm) ~ time * factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl0.narm)
##
## Call:
## glm(formula = cbind(V1, notV1.narm) ~ time * factor(ageClass),
## family = "binomial", data = dat.France.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -4.0694 -1.0888 0.0445 1.1808 6.5207
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.272629 0.015719 17.344 < 2e-16 ***
## time 0.049916 0.001598 31.232 < 2e-16 ***
## factor(ageClass)14.5 -0.189098 0.018013 -10.498 < 2e-16 ***
## factor(ageClass)24.5 -0.249451 0.017769 -14.039 < 2e-16 ***
## factor(ageClass)34.5 -0.172360 0.017729 -9.722 < 2e-16 ***
## factor(ageClass)44.5 -0.175171 0.017692 -9.901 < 2e-16 ***
## factor(ageClass)54.5 -0.292472 0.017849 -16.386 < 2e-16 ***
## factor(ageClass)64.5 -0.417649 0.018624 -22.425 < 2e-16 ***
## factor(ageClass)74.5 -0.697555 0.020196 -34.539 < 2e-16 ***
## factor(ageClass)84.5 -0.973347 0.021578 -45.108 < 2e-16 ***
## factor(ageClass)94.5 -1.129383 0.026191 -43.121 < 2e-16 ***
## time:factor(ageClass)14.5 0.005881 0.001831 3.211 0.001321 **
## time:factor(ageClass)24.5 0.011331 0.001807 6.269 3.63e-10 ***
## time:factor(ageClass)34.5 0.005380 0.001806 2.979 0.002896 **
## time:factor(ageClass)44.5 0.005041 0.001804 2.794 0.005204 **
## time:factor(ageClass)54.5 0.006868 0.001818 3.778 0.000158 ***
## time:factor(ageClass)64.5 0.006843 0.001890 3.620 0.000295 ***
## time:factor(ageClass)74.5 0.022417 0.002053 10.921 < 2e-16 ***
## time:factor(ageClass)84.5 0.022285 0.002218 10.046 < 2e-16 ***
## time:factor(ageClass)94.5 0.018750 0.002762 6.787 1.14e-11 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 50201.02 on 179 degrees of freedom
## Residual deviance: 615.12 on 160 degrees of freedom
## AIC: 2327.9
##
## Number of Fisher Scoring iterations: 3
# Without interaction
mdl1.narm <- glm(cbind(V1, notV1.narm) ~ time + factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl1.narm)
##
## Call:
## glm(formula = cbind(V1, notV1.narm) ~ time + factor(ageClass),
## family = "binomial", data = dat.France.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -6.3553 -1.3565 0.1452 1.2478 7.6394
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.2007295 0.0085771 23.40 <2e-16 ***
## time 0.0584876 0.0003257 179.57 <2e-16 ***
## factor(ageClass)14.5 -0.1399048 0.0093042 -15.04 <2e-16 ***
## factor(ageClass)24.5 -0.1542727 0.0091738 -16.82 <2e-16 ***
## factor(ageClass)34.5 -0.1270116 0.0091778 -13.84 <2e-16 ***
## factor(ageClass)44.5 -0.1325456 0.0091581 -14.47 <2e-16 ***
## factor(ageClass)54.5 -0.2348562 0.0092135 -25.49 <2e-16 ***
## factor(ageClass)64.5 -0.3604909 0.0095800 -37.63 <2e-16 ***
## factor(ageClass)74.5 -0.5078669 0.0103394 -49.12 <2e-16 ***
## factor(ageClass)84.5 -0.7889338 0.0111574 -70.71 <2e-16 ***
## factor(ageClass)94.5 -0.9776377 0.0138001 -70.84 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 50201.02 on 179 degrees of freedom
## Residual deviance: 919.41 on 169 degrees of freedom
## AIC: 2614.2
##
## Number of Fisher Scoring iterations: 3
## Likelihood ratio test
anova(mdl1.narm, mdl0.narm, test="Chisq")
## Analysis of Deviance Table
##
## Model 1: cbind(V1, notV1.narm) ~ time + factor(ageClass)
## Model 2: cbind(V1, notV1.narm) ~ time * factor(ageClass)
## Resid. Df Resid. Dev Df Deviance Pr(>Chi)
## 1 169 919.41
## 2 160 615.12 9 304.3 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# Test date effect
mdl2.narm <- glm(cbind(V1, notV1.narm) ~ time * ageClass, data = dat.France.ages, family = "binomial")
summary(mdl2.narm)
##
## Call:
## glm(formula = cbind(V1, notV1.narm) ~ time * ageClass, family = "binomial",
## data = dat.France.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -12.0104 -5.3925 -0.5634 3.0613 12.6203
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 3.522e-01 6.894e-03 51.09 <2e-16 ***
## time 5.061e-02 7.079e-04 71.50 <2e-16 ***
## ageClass -9.205e-03 1.419e-04 -64.89 <2e-16 ***
## time:ageClass 1.897e-04 1.466e-05 12.94 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 50201.0 on 179 degrees of freedom
## Residual deviance: 5018.8 on 176 degrees of freedom
## AIC: 6699.6
##
## Number of Fisher Scoring iterations: 3
## Likelihood ratio test
anova(mdl2.narm, mdl0.narm, test="Chisq")
## Analysis of Deviance Table
##
## Model 1: cbind(V1, notV1.narm) ~ time * ageClass
## Model 2: cbind(V1, notV1.narm) ~ time * factor(ageClass)
## Resid. Df Resid. Dev Df Deviance Pr(>Chi)
## 1 176 5018.8
## 2 160 615.1 16 4403.7 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# All ages, time
par(las = 1)
plot(dat.France$date2, dat.France$Prc_susp_501Y_V2_3, ylim = c(0, 100),
col = colsAge[as.character(dat.France$cl_age90)],
pch = pchAge[as.character(dat.France$cl_age90)],
cex = cexAge[as.character(dat.France$cl_age90)],
xlab = "date", ylab = "Proportion V2/V3", axes = FALSE)
axis(1, pos = 0, at = as.Date(unique(dat.France$date2)), labels = format(unique(dat.France$date2), format = "%b %d"))
axis(2)
Binomial
# Create new colums with information on number of specific PCR tests
# PCR with V2/V3 result
dat.France.ages$V23 <- dat.France.ages$Nb_susp_501Y_V2_3
# All other PCRs (considering NAs are non-V23)
dat.France.ages$notV23 <- dat.France.ages$Nb_tests_PCR_TA_crible - dat.France.ages$Nb_susp_501Y_V2_3
# All other PCRs with a result (removing NAs)
dat.France.ages$notV23.narm <- dat.France.ages$Nb_susp_501Y_V1 + dat.France.ages$Nb_susp_ABS
# GLM
# Assuming that all IND (indetermine) are non-V23
mdl0 <- glm(cbind(V23, notV23) ~ time * factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl0)
##
## Call:
## glm(formula = cbind(V23, notV23) ~ time * factor(ageClass), family = "binomial",
## data = dat.France.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -3.2343 -0.8336 -0.0472 0.7092 3.0681
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.101e+00 3.501e-02 -88.564 < 2e-16 ***
## time 6.063e-03 3.386e-03 1.790 0.07338 .
## factor(ageClass)14.5 2.491e-01 3.946e-02 6.312 2.76e-10 ***
## factor(ageClass)24.5 2.582e-01 3.897e-02 6.624 3.49e-11 ***
## factor(ageClass)34.5 3.928e-02 3.937e-02 0.998 0.31835
## factor(ageClass)44.5 2.848e-02 3.943e-02 0.722 0.47008
## factor(ageClass)54.5 5.972e-02 3.967e-02 1.505 0.13223
## factor(ageClass)64.5 2.046e-01 4.082e-02 5.012 5.38e-07 ***
## factor(ageClass)74.5 -2.533e-01 4.720e-02 -5.366 8.06e-08 ***
## factor(ageClass)84.5 -3.326e-01 5.142e-02 -6.468 9.90e-11 ***
## factor(ageClass)94.5 -2.731e-01 6.156e-02 -4.436 9.17e-06 ***
## time:factor(ageClass)14.5 -6.631e-03 3.830e-03 -1.731 0.08339 .
## time:factor(ageClass)24.5 -9.150e-03 3.785e-03 -2.418 0.01563 *
## time:factor(ageClass)34.5 1.080e-02 3.802e-03 2.841 0.00449 **
## time:factor(ageClass)44.5 5.700e-03 3.819e-03 1.493 0.13552
## time:factor(ageClass)54.5 6.660e-03 3.841e-03 1.734 0.08293 .
## time:factor(ageClass)64.5 -8.279e-06 3.960e-03 -0.002 0.99833
## time:factor(ageClass)74.5 1.245e-02 4.559e-03 2.730 0.00633 **
## time:factor(ageClass)84.5 9.013e-03 5.099e-03 1.767 0.07715 .
## time:factor(ageClass)94.5 1.210e-02 6.311e-03 1.918 0.05517 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 1702.41 on 179 degrees of freedom
## Residual deviance: 315.07 on 160 degrees of freedom
## AIC: 1747.5
##
## Number of Fisher Scoring iterations: 3
# Without interaction
mdl1 <- glm(cbind(V23, notV23) ~ time + factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl1)
##
## Call:
## glm(formula = cbind(V23, notV23) ~ time + factor(ageClass), family = "binomial",
## data = dat.France.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -4.8227 -1.0518 0.1092 0.9814 3.2845
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.1198628 0.0183534 -169.988 < 2e-16 ***
## time 0.0081962 0.0006807 12.040 < 2e-16 ***
## factor(ageClass)14.5 0.1901572 0.0195394 9.732 < 2e-16 ***
## factor(ageClass)24.5 0.1770289 0.0193008 9.172 < 2e-16 ***
## factor(ageClass)34.5 0.1366049 0.0193766 7.050 1.79e-12 ***
## factor(ageClass)44.5 0.0794749 0.0194558 4.085 4.41e-05 ***
## factor(ageClass)54.5 0.1193852 0.0195467 6.108 1.01e-09 ***
## factor(ageClass)64.5 0.2047544 0.0201562 10.158 < 2e-16 ***
## factor(ageClass)74.5 -0.1416976 0.0231138 -6.130 8.76e-10 ***
## factor(ageClass)84.5 -0.2556056 0.0259329 -9.856 < 2e-16 ***
## factor(ageClass)94.5 -0.1746847 0.0319622 -5.465 4.62e-08 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 1702.41 on 179 degrees of freedom
## Residual deviance: 438.73 on 169 degrees of freedom
## AIC: 1853.2
##
## Number of Fisher Scoring iterations: 3
## Likelihood ratio test
anova(mdl1, mdl0, test="Chisq")
## Analysis of Deviance Table
##
## Model 1: cbind(V23, notV23) ~ time + factor(ageClass)
## Model 2: cbind(V23, notV23) ~ time * factor(ageClass)
## Resid. Df Resid. Dev Df Deviance Pr(>Chi)
## 1 169 438.73
## 2 160 315.07 9 123.67 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# Test date effect
mdl2 <- glm(cbind(V23, notV23) ~ time * ageClass, data = dat.France.ages, family = "binomial")
summary(mdl2)
##
## Call:
## glm(formula = cbind(V23, notV23) ~ time * ageClass, family = "binomial",
## data = dat.France.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -4.5268 -2.5430 -0.9477 1.3786 5.1717
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.810e+00 1.464e-02 -192.018 < 2e-16 ***
## time -1.128e-03 1.435e-03 -0.786 0.432
## ageClass -5.004e-03 3.132e-04 -15.975 < 2e-16 ***
## time:ageClass 2.347e-04 3.085e-05 7.609 2.76e-14 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 1702.4 on 179 degrees of freedom
## Residual deviance: 1117.2 on 176 degrees of freedom
## AIC: 2517.6
##
## Number of Fisher Scoring iterations: 4
## Likelihood ratio test
anova(mdl2, mdl0, test="Chisq")
## Analysis of Deviance Table
##
## Model 1: cbind(V23, notV23) ~ time * ageClass
## Model 2: cbind(V23, notV23) ~ time * factor(ageClass)
## Resid. Df Resid. Dev Df Deviance Pr(>Chi)
## 1 176 1117.16
## 2 160 315.07 16 802.1 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# GLM
# Assuming that all IND (indetermine) are non-V23
mdl0.narm <- glm(cbind(V23, notV23.narm) ~ time * factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl0.narm)
##
## Call:
## glm(formula = cbind(V23, notV23.narm) ~ time * factor(ageClass),
## family = "binomial", data = dat.France.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -3.1803 -0.7890 -0.0710 0.7139 3.0180
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.9887015 0.0351726 -84.972 < 2e-16 ***
## time 0.0057683 0.0034042 1.694 0.09018 .
## factor(ageClass)14.5 0.2261837 0.0396327 5.707 1.15e-08 ***
## factor(ageClass)24.5 0.2427125 0.0391383 6.201 5.60e-10 ***
## factor(ageClass)34.5 0.0200154 0.0395290 0.506 0.61261
## factor(ageClass)44.5 0.0057322 0.0395889 0.145 0.88487
## factor(ageClass)54.5 0.0405250 0.0398441 1.017 0.30911
## factor(ageClass)64.5 0.1897116 0.0409918 4.628 3.69e-06 ***
## factor(ageClass)74.5 -0.2536145 0.0473419 -5.357 8.46e-08 ***
## factor(ageClass)84.5 -0.3257049 0.0515909 -6.313 2.73e-10 ***
## factor(ageClass)94.5 -0.2713405 0.0617731 -4.393 1.12e-05 ***
## time:factor(ageClass)14.5 -0.0065839 0.0038484 -1.711 0.08711 .
## time:factor(ageClass)24.5 -0.0089406 0.0038028 -2.351 0.01872 *
## time:factor(ageClass)34.5 0.0110257 0.0038192 2.887 0.00389 **
## time:factor(ageClass)44.5 0.0056161 0.0038363 1.464 0.14321
## time:factor(ageClass)54.5 0.0062869 0.0038597 1.629 0.10334
## time:factor(ageClass)64.5 -0.0003364 0.0039785 -0.085 0.93262
## time:factor(ageClass)74.5 0.0119004 0.0045732 2.602 0.00926 **
## time:factor(ageClass)84.5 0.0090968 0.0051181 1.777 0.07551 .
## time:factor(ageClass)94.5 0.0133106 0.0063357 2.101 0.03565 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 1555.35 on 179 degrees of freedom
## Residual deviance: 308.18 on 160 degrees of freedom
## AIC: 1739.8
##
## Number of Fisher Scoring iterations: 3
# Without interaction
mdl1.narm <- glm(cbind(V23, notV23.narm) ~ time + factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl1.narm)
##
## Call:
## glm(formula = cbind(V23, notV23.narm) ~ time + factor(ageClass),
## family = "binomial", data = dat.France.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -4.7997 -1.0008 0.0805 0.9932 3.2320
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.0077065 0.0184010 -163.454 < 2e-16 ***
## time 0.0078766 0.0006825 11.541 < 2e-16 ***
## factor(ageClass)14.5 0.1676880 0.0195899 8.560 < 2e-16 ***
## factor(ageClass)24.5 0.1634677 0.0193516 8.447 < 2e-16 ***
## factor(ageClass)34.5 0.1193159 0.0194269 6.142 8.16e-10 ***
## factor(ageClass)44.5 0.0559718 0.0195050 2.870 0.00411 **
## factor(ageClass)54.5 0.0968684 0.0195965 4.943 7.69e-07 ***
## factor(ageClass)64.5 0.1869081 0.0202091 9.249 < 2e-16 ***
## factor(ageClass)74.5 -0.1468689 0.0231697 -6.339 2.32e-10 ***
## factor(ageClass)84.5 -0.2480370 0.0259946 -9.542 < 2e-16 ***
## factor(ageClass)94.5 -0.1635410 0.0320422 -5.104 3.33e-07 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 1555.35 on 179 degrees of freedom
## Residual deviance: 429.68 on 169 degrees of freedom
## AIC: 1843.3
##
## Number of Fisher Scoring iterations: 3
## Likelihood ratio test
anova(mdl1.narm, mdl0.narm, test="Chisq")
## Analysis of Deviance Table
##
## Model 1: cbind(V23, notV23.narm) ~ time + factor(ageClass)
## Model 2: cbind(V23, notV23.narm) ~ time * factor(ageClass)
## Resid. Df Resid. Dev Df Deviance Pr(>Chi)
## 1 169 429.68
## 2 160 308.18 9 121.5 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# Test date effect
mdl2.narm <- glm(cbind(V23, notV23.narm) ~ time * ageClass, data = dat.France.ages, family = "binomial")
summary(mdl2.narm)
##
## Call:
## glm(formula = cbind(V23, notV23.narm) ~ time * ageClass, family = "binomial",
## data = dat.France.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -4.1401 -2.4294 -0.7728 1.2912 5.1410
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.721e+00 1.472e-02 -184.888 < 2e-16 ***
## time -1.211e-03 1.444e-03 -0.838 0.402
## ageClass -4.826e-03 3.152e-04 -15.311 < 2e-16 ***
## time:ageClass 2.284e-04 3.105e-05 7.354 1.93e-13 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 1555.4 on 179 degrees of freedom
## Residual deviance: 1021.6 on 176 degrees of freedom
## AIC: 2421.2
##
## Number of Fisher Scoring iterations: 4
## Likelihood ratio test
anova(mdl2.narm, mdl0.narm, test="Chisq")
## Analysis of Deviance Table
##
## Model 1: cbind(V23, notV23.narm) ~ time * ageClass
## Model 2: cbind(V23, notV23.narm) ~ time * factor(ageClass)
## Resid. Df Resid. Dev Df Deviance Pr(>Chi)
## 1 176 1021.62
## 2 160 308.18 16 713.44 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Prepare plots for distribution of variants
par(mfrow = c(1, 1))
getVec <- function(dataset, prop = TRUE){
if(prop){
nn <- 1
}else{
nn <- dataset$Nb_tests_POS / 7 # Divide by 7 to have average over the week instead of sum
}
x <- dataset$date2
c1 <- dataset$Prc_susp_501Y_V1/100 * nn
c23 <- c1 + dataset$Prc_susp_501Y_V2_3/100 * nn
cABS <- c23 + dataset$Prc_susp_ABS/100 * nn
cIND <- cABS + dataset$Prc_susp_IND/100 * nn
list(x = x, c1 = c1, c23 = c23, cABS = cABS, cIND = cIND)
}
colV <- c(brewer.pal(3, "Set2"), gray(0.5))
plotDist <- function(x, c1, c23, cABS, cIND){
if(max(cIND, na.rm = TRUE) == 1 | max(cIND, na.rm = TRUE) == 100 | max(c1, na.rm = TRUE) > 100){
yl <- "Proportions variants"
}else{
yl <- "Number cases"
}
plot(x, c1, ylim = c(0, max(cIND)), type = "l",
xlab = "date", ylab = yl, axes = FALSE)
axis(1, pos = 0, labels = format(x, "%b-%d"), at = x)
axis(2, pos = x[1])
polygon(c(x, rev(x)), c(rep(0, length(x)), rev(c1)), col = colV[1], border = NULL)
polygon(c(x, rev(x)), c(c1, rev(c23)), col = colV[2], border = NULL)
polygon(c(x, rev(x)), c(c23, rev(cABS)), col = colV[3], border = NULL)
polygon(c(x, rev(x)), c(cABS, rev(cIND)), col = colV[4], border = NULL)
nend <- length(x)-1
text(x = rep(x[nend], 4), y = c(c1[nend]/2, c1[nend] + (c23[nend] - c1[nend])/2, c23[nend] + (cABS[nend] - c23[nend])/2, cABS[nend] + (cIND[nend] - cABS[nend])/2), labels = c("V1", "V2/V3", "WT", "indet."), col = "white", adj = 1)
}
Frequencies
cc <- getVec(dat.France.0, prop = TRUE)
plotDist(cc$x, cc$c1, cc$c23, cc$cABS, cc$cIND)
Densities
cc <- getVec(dat.France.0, prop = FALSE)
plotDist(cc$x, cc$c1, cc$c23, cc$cABS, cc$cIND)
mat <- as.matrix(data.frame(WT = dat.France.ages$Nb_susp_ABS,
V1 = dat.France.ages$Nb_susp_501Y_V1,
V2 = dat.France.ages$Nb_susp_501Y_V2_3,
INDET = dat.France.ages$Nb_susp_IND))
library(nnet)
## Null model
m0 <- multinom(mat ~ 1)
## # weights: 8 (3 variable)
## initial value 2460671.104693
## final value 1855506.003454
## converged
summary(m0)
## Call:
## multinom(formula = mat ~ 1)
##
## Coefficients:
## (Intercept)
## V1 0.6119623
## V2 -1.8046807
## INDET -1.2781219
##
## Std. Errors:
## (Intercept)
## V1 0.001690021
## V2 0.003620477
## INDET 0.002915485
##
## Residual Deviance: 3711012
## AIC: 3711018
## Compute by hand to check result
log(colSums(mat)[2]/colSums(mat)[1])
## V1
## 0.6120011
log(colSums(mat)[3]/colSums(mat)[1])
## V2
## -1.804692
log(colSums(mat)[4]/colSums(mat)[1])
## INDET
## -1.277982
## Time effect
m1 <- multinom(mat ~ time, data=dat.France.ages)
## # weights: 12 (6 variable)
## initial value 2460671.104693
## iter 10 value 1835784.719195
## final value 1835774.796613
## converged
summary(m1)
## Call:
## multinom(formula = mat ~ time, data = dat.France.ages)
##
## Coefficients:
## (Intercept) time
## V1 0.04833576 0.06676898
## V2 -2.23282492 0.05187632
## INDET -1.59432367 0.03910026
##
## Std. Errors:
## (Intercept) time
## V1 0.003277047 0.0003410188
## V2 0.007259751 0.0007204104
## INDET 0.005663837 0.0005796311
##
## Residual Deviance: 3671550
## AIC: 3671562
## Likelihood ratio test
anova(m0, m1, test="Chisq")
## Model Resid. df Resid. Dev Test Df LR stat. Pr(Chi)
## 1 1 537 3711012 NA NA NA
## 2 time 534 3671550 1 vs 2 3 39462.41 0
## Age effect
m2 <- multinom(mat ~ time + stdage, data=dat.France.ages)
## # weights: 16 (9 variable)
## initial value 2460671.104693
## iter 10 value 1853648.120734
## final value 1834148.253751
## converged
summary(m2)
## Call:
## multinom(formula = mat ~ time + stdage, data = dat.France.ages)
##
## Coefficients:
## (Intercept) time stdage
## V1 0.008541788 0.06662480 -0.04747537
## V2 -2.261699066 0.05177393 -0.03549250
## INDET -1.629594672 0.03897770 -0.04254707
##
## Std. Errors:
## (Intercept) time stdage
## V1 0.003355564 0.0003413456 0.0008613089
## V2 0.007412590 0.0007205136 0.0017311923
## INDET 0.005793389 0.0005797807 0.0013831851
##
## Residual Deviance: 3668297
## AIC: 3668315
## Likelihood ratio test
anova(m1, m2, test="Chisq")
## Model Resid. df Resid. Dev Test Df LR stat. Pr(Chi)
## 1 time 534 3671550 NA NA NA
## 2 time + stdage 531 3668297 1 vs 2 3 3253.086 0
## Age effect
m3 <- multinom(mat ~ time * stdage, data=dat.France.ages)
## # weights: 20 (12 variable)
## initial value 2460671.104693
## iter 10 value 1924569.724771
## iter 20 value 1834100.956963
## final value 1834100.925004
## converged
summary(m3)
## Call:
## multinom(formula = mat ~ time * stdage, data = dat.France.ages)
##
## Coefficients:
## (Intercept) time stdage time:stdage
## V1 -0.001225914 0.06782063 -0.05896115 1.402145e-03
## V2 -2.273416450 0.05321451 -0.04936935 1.694381e-03
## INDET -1.626780979 0.03873798 -0.04086087 -8.504092e-05
##
## Std. Errors:
## (Intercept) time stdage time:stdage
## V1 0.003550246 0.0003703003 0.001631136 0.0001694933
## V2 0.007881503 0.0007836125 0.003401622 0.0003402115
## INDET 0.006143479 0.0006308728 0.002696711 0.0002720972
##
## Residual Deviance: 3668202
## AIC: 3668226
## Likelihood ratio test
anova(m2, m3, test="Chisq")
## Model Resid. df Resid. Dev Test Df LR stat. Pr(Chi)
## 1 time + stdage 531 3668297 NA NA NA
## 2 time * stdage 528 3668202 1 vs 2 3 94.65749 0
Pb in the data is the change in the age structure of positive individuals; to really test the effet, we would need information on the negative tests as well, and the age distribution in these negative tests.
tapply(dat.France.ages$Nb_tests_PCR_TA_crible, list(dat.France.ages$cl_age90, dat.France.ages$time), sum)
## 0 1 2 3 4 5 6 7 8 9 10 11
## 9 3564 3813 3912 3941 4008 4095 4234 4328 4475 4495 4482 4518
## 19 10508 11441 11845 11909 12446 12826 13136 13452 13654 13682 13722 13845
## 29 11675 12907 13335 13458 14294 14853 15206 15457 15499 15638 15666 15751
## 39 12290 13317 13784 13833 14486 14998 15237 15496 15580 15556 15616 15690
## 49 12409 13542 14010 14130 14825 15339 15693 15763 15843 15952 15958 15935
## 59 11174 12289 12777 12874 13663 14167 14501 14816 14911 14916 14913 14791
## 69 8010 8781 9038 9106 9586 9918 10244 10491 10533 10660 10655 10723
## 79 5152 5589 5813 5887 6063 6374 6543 6614 6675 6680 6649 6676
## 89 4291 4601 4706 4773 4788 4775 4756 4644 4596 4562 4545 4373
## 90 2385 2472 2520 2551 2503 2470 2358 2281 2203 2182 2170 1991
## 12 13 14 15 16 17
## 9 4563 4546 4610 4571 4539 4544
## 19 13869 13936 13848 13676 13613 13580
## 29 15881 15885 15857 15579 15427 15334
## 39 15562 15575 15324 15005 14952 14868
## 49 15760 15594 15464 14928 14723 14634
## 59 14654 14450 14122 13734 13542 13487
## 69 10707 10529 10348 10089 9902 9810
## 79 6537 6410 6254 6073 5991 5940
## 89 4264 4079 3939 3750 3650 3591
## 90 1863 1751 1634 1553 1521 1478
URL <- "https://www.data.gouv.fr/fr/datasets/r/73e8851a-d851-43f8-89e4-6178b35b7127"
dataFile <- paste0("data/Regions_", today, ".csv") # name file with today's date
download.file(URL, dataFile) # download file from repo
dat.regions <- read.csv(dataFile, sep = ";", stringsAsFactors = FALSE)
# Format date
dat.regions$date1 <- as.Date(substring(dat.regions$semaine, 1, 10))
dat.regions$date2 <- as.Date(substring(dat.regions$semaine, 12, 21))
# Rewrite time as days since beginning of the data
dat.regions$time <- dat.regions$date2 - min(dat.regions$date2)
# Compute data on total tests
dat.regions$Nb_tests_POS <- dat.regions$Nb_tests_PCR_TA_crible / (dat.regions$Prc_tests_PCR_TA_crible / 100)
# Codes regions
URL <- "https://www.data.gouv.fr/en/datasets/r/34fc7b52-ef11-4ab0-bc16-e1aae5c942e7"
dataFile <- "data/coderegions.csv"
download.file(URL, dataFile)
codesRegions <- read.csv(dataFile, sep = ",", stringsAsFactors = FALSE)
# Turn into dictionary
regs <- codesRegions$nom_region
names(regs) <- as.character(codesRegions$code_region)
# Add region name
dat.regions$reg_name <- regs[as.character(dat.regions$reg)]
# dat.regions[floor(runif(10)*1000), c("reg", "reg_name")] # check a few names
# What are the other regions??
# aggregate(dat.regions$reg, by = list(dat.regions$reg), FUN = length)
Format data further
dat.regions.ages <- dat.regions[dat.regions$cl_age90 != 0,]
# Add new age class code -- median of the age class
dat.regions.ages$ageClass <- dic.age[as.character(dat.regions.ages$cl_age90)]
# Standardize age class values
dat.regions.ages$stdage <- (dat.regions.ages$ageClass - mean(dat.regions.ages$ageClass))/dat.regions.ages$ageClass
tmp <- unique(dat.regions$reg) # Region codes
tmp <- tmp[tmp>10 & tmp <= 93] # Choose only metropolitan regions
par(mfrow = c(4, 3))
for(region in tmp){
subdat <- dat.regions[dat.regions$reg == region, ]
plot(subdat$date2, subdat$Prc_susp_501Y_V1, ylim = c(0, 100), main = regs[as.character(region)], col = colsAge[as.character(subdat$cl_age90)], pch = pchAge[as.character(subdat$cl_age90)],
xlab = "date", ylab = "Proportion V1"
)
}
# Create new colums with information on number of specific PCR tests
# PCR with V1 result
dat.regions.ages$V1 <- dat.regions.ages$Nb_susp_501Y_V1
# All other PCRs (considering NAs are non-V1)
dat.regions.ages$notV1 <- dat.regions.ages$Nb_tests_PCR_TA_crible - dat.regions.ages$Nb_susp_501Y_V1
# All other PCRs with a result (removing NAs)
dat.regions.ages$notV1.narm <- dat.regions.ages$Nb_susp_501Y_V2_3 + dat.regions.ages$Nb_susp_ABS
# Check that columns currently sum
all(dat.regions.ages$Nb_susp_501Y_V2_3 + dat.regions.ages$Nb_susp_ABS + dat.regions.ages$Nb_susp_501Y_V1 + dat.regions.ages$Nb_susp_IND - dat.regions.ages$Nb_tests_PCR_TA_crible == 0)
## [1] TRUE
dat.regions.ages$reg_name.fac <- as.factor(dat.regions.ages$reg_name)
# GLM
# Assuming that all IND (indetermine) are non-V1
mdl0 <- glm(cbind(V1, notV1) ~ time * factor(ageClass) * factor(reg_name), data = dat.regions.ages, family = "binomial")
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
summary(mdl0)
##
## Call:
## glm(formula = cbind(V1, notV1) ~ time * factor(ageClass) * factor(reg_name),
## family = "binomial", data = dat.regions.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -3.2242 -0.4580 0.0000 0.4603 4.0993
##
## Coefficients: (11 not defined because of singularities)
## Estimate
## (Intercept) -1.684e-01
## time 5.144e-02
## factor(ageClass)14.5 -5.234e-03
## factor(ageClass)24.5 -2.009e-01
## factor(ageClass)34.5 -1.763e-01
## factor(ageClass)44.5 -2.080e-01
## factor(ageClass)54.5 -3.267e-01
## factor(ageClass)64.5 -5.585e-01
## factor(ageClass)74.5 -6.705e-01
## factor(ageClass)84.5 -9.681e-01
## factor(ageClass)94.5 -1.127e+00
## factor(reg_name)Bourgogne-Franche-Comté -5.311e-01
## factor(reg_name)Bretagne 6.454e-01
## factor(reg_name)Centre-Val de Loire -2.424e-02
## factor(reg_name)Corse 2.778e+00
## factor(reg_name)Grand Est -6.609e-01
## factor(reg_name)Guadeloupe -1.627e+02
## factor(reg_name)Guyane -1.840e+01
## factor(reg_name)Hauts-de-France 4.812e-01
## factor(reg_name)ÃŽle-de-France 5.822e-01
## factor(reg_name)La Réunion -3.214e+00
## factor(reg_name)Martinique -2.733e+00
## factor(reg_name)Mayotte 1.986e+01
## factor(reg_name)Normandie -1.129e-01
## factor(reg_name)Nouvelle-Aquitaine 2.153e-01
## factor(reg_name)Occitanie 2.685e-01
## factor(reg_name)Pays de la Loire -2.237e-01
## factor(reg_name)Provence-Alpes-Côte d'Azur 4.653e-01
## time:factor(ageClass)14.5 -1.328e-02
## time:factor(ageClass)24.5 2.605e-03
## time:factor(ageClass)34.5 7.452e-03
## time:factor(ageClass)44.5 7.543e-03
## time:factor(ageClass)54.5 8.898e-03
## time:factor(ageClass)64.5 2.118e-02
## time:factor(ageClass)74.5 2.215e-02
## time:factor(ageClass)84.5 3.985e-03
## time:factor(ageClass)94.5 -2.083e-03
## time:factor(reg_name)Bourgogne-Franche-Comté 6.228e-03
## time:factor(reg_name)Bretagne -2.416e-02
## time:factor(reg_name)Centre-Val de Loire 1.709e-02
## time:factor(reg_name)Corse -1.756e-01
## time:factor(reg_name)Grand Est -1.913e-03
## time:factor(reg_name)Guadeloupe 1.482e+01
## time:factor(reg_name)Guyane -5.144e-02
## time:factor(reg_name)Hauts-de-France -1.587e-02
## time:factor(reg_name)ÃŽle-de-France -2.154e-02
## time:factor(reg_name)La Réunion 2.709e-02
## time:factor(reg_name)Martinique 2.267e-01
## time:factor(reg_name)Mayotte -4.936e-02
## time:factor(reg_name)Normandie 2.722e-04
## time:factor(reg_name)Nouvelle-Aquitaine -2.315e-02
## time:factor(reg_name)Occitanie 6.928e-03
## time:factor(reg_name)Pays de la Loire 2.532e-03
## time:factor(reg_name)Provence-Alpes-Côte d'Azur 3.999e-03
## factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté -1.788e-01
## factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté 1.990e-01
## factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté 4.100e-02
## factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté -9.000e-02
## factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté -1.143e-01
## factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté 1.118e-01
## factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté 1.524e-01
## factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté 2.405e-01
## factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté 7.230e-02
## factor(ageClass)14.5:factor(reg_name)Bretagne -1.945e-01
## factor(ageClass)24.5:factor(reg_name)Bretagne -2.708e-01
## factor(ageClass)34.5:factor(reg_name)Bretagne -2.008e-01
## factor(ageClass)44.5:factor(reg_name)Bretagne 4.305e-02
## factor(ageClass)54.5:factor(reg_name)Bretagne 4.058e-02
## factor(ageClass)64.5:factor(reg_name)Bretagne -1.127e-01
## factor(ageClass)74.5:factor(reg_name)Bretagne 1.373e-01
## factor(ageClass)84.5:factor(reg_name)Bretagne 6.214e-02
## factor(ageClass)94.5:factor(reg_name)Bretagne 1.337e-01
## factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire -3.655e-03
## factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire 7.279e-02
## factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire 1.831e-01
## factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire 2.015e-01
## factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire 1.548e-01
## factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire 2.948e-01
## factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire -1.207e-01
## factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire 2.110e-01
## factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire 4.211e-02
## factor(ageClass)14.5:factor(reg_name)Corse -2.492e+00
## factor(ageClass)24.5:factor(reg_name)Corse -1.901e+00
## factor(ageClass)34.5:factor(reg_name)Corse -2.200e+00
## factor(ageClass)44.5:factor(reg_name)Corse -1.425e+00
## factor(ageClass)54.5:factor(reg_name)Corse -1.302e+00
## factor(ageClass)64.5:factor(reg_name)Corse -1.611e+00
## factor(ageClass)74.5:factor(reg_name)Corse -1.587e+00
## factor(ageClass)84.5:factor(reg_name)Corse -5.760e-01
## factor(ageClass)94.5:factor(reg_name)Corse 1.307e+01
## factor(ageClass)14.5:factor(reg_name)Grand Est -2.821e-01
## factor(ageClass)24.5:factor(reg_name)Grand Est 1.975e-01
## factor(ageClass)34.5:factor(reg_name)Grand Est 1.894e-01
## factor(ageClass)44.5:factor(reg_name)Grand Est 2.051e-01
## factor(ageClass)54.5:factor(reg_name)Grand Est 2.888e-01
## factor(ageClass)64.5:factor(reg_name)Grand Est 4.306e-01
## factor(ageClass)74.5:factor(reg_name)Grand Est 1.793e-01
## factor(ageClass)84.5:factor(reg_name)Grand Est 2.118e-01
## factor(ageClass)94.5:factor(reg_name)Grand Est 3.312e-01
## factor(ageClass)14.5:factor(reg_name)Guadeloupe 1.634e+02
## factor(ageClass)24.5:factor(reg_name)Guadeloupe 1.642e+02
## factor(ageClass)34.5:factor(reg_name)Guadeloupe 1.627e+02
## factor(ageClass)44.5:factor(reg_name)Guadeloupe 1.645e+02
## factor(ageClass)54.5:factor(reg_name)Guadeloupe 1.640e+02
## factor(ageClass)64.5:factor(reg_name)Guadeloupe 1.629e+02
## factor(ageClass)74.5:factor(reg_name)Guadeloupe 1.662e+02
## factor(ageClass)84.5:factor(reg_name)Guadeloupe 1.824e+02
## factor(ageClass)94.5:factor(reg_name)Guadeloupe NA
## factor(ageClass)14.5:factor(reg_name)Guyane -8.620e-01
## factor(ageClass)24.5:factor(reg_name)Guyane 1.703e+01
## factor(ageClass)34.5:factor(reg_name)Guyane -5.027e+01
## factor(ageClass)44.5:factor(reg_name)Guyane 1.906e+01
## factor(ageClass)54.5:factor(reg_name)Guyane 2.471e+01
## factor(ageClass)64.5:factor(reg_name)Guyane 3.717e-01
## factor(ageClass)74.5:factor(reg_name)Guyane NA
## factor(ageClass)84.5:factor(reg_name)Guyane 9.681e-01
## factor(ageClass)94.5:factor(reg_name)Guyane NA
## factor(ageClass)14.5:factor(reg_name)Hauts-de-France -1.881e-01
## factor(ageClass)24.5:factor(reg_name)Hauts-de-France 6.888e-02
## factor(ageClass)34.5:factor(reg_name)Hauts-de-France 9.802e-02
## factor(ageClass)44.5:factor(reg_name)Hauts-de-France 7.353e-02
## factor(ageClass)54.5:factor(reg_name)Hauts-de-France 1.498e-01
## factor(ageClass)64.5:factor(reg_name)Hauts-de-France 3.101e-01
## factor(ageClass)74.5:factor(reg_name)Hauts-de-France 2.925e-01
## factor(ageClass)84.5:factor(reg_name)Hauts-de-France 3.441e-01
## factor(ageClass)94.5:factor(reg_name)Hauts-de-France 3.465e-01
## factor(ageClass)14.5:factor(reg_name)ÃŽle-de-France -2.010e-02
## factor(ageClass)24.5:factor(reg_name)ÃŽle-de-France -8.495e-02
## factor(ageClass)34.5:factor(reg_name)ÃŽle-de-France 7.803e-02
## factor(ageClass)44.5:factor(reg_name)ÃŽle-de-France 1.346e-01
## factor(ageClass)54.5:factor(reg_name)ÃŽle-de-France 1.450e-01
## factor(ageClass)64.5:factor(reg_name)ÃŽle-de-France 2.914e-01
## factor(ageClass)74.5:factor(reg_name)ÃŽle-de-France 9.173e-02
## factor(ageClass)84.5:factor(reg_name)ÃŽle-de-France -2.640e-01
## factor(ageClass)94.5:factor(reg_name)ÃŽle-de-France -6.607e-02
## factor(ageClass)14.5:factor(reg_name)La Réunion 1.009e+00
## factor(ageClass)24.5:factor(reg_name)La Réunion -1.447e+00
## factor(ageClass)34.5:factor(reg_name)La Réunion 1.421e+00
## factor(ageClass)44.5:factor(reg_name)La Réunion 1.346e+00
## factor(ageClass)54.5:factor(reg_name)La Réunion 1.448e+00
## factor(ageClass)64.5:factor(reg_name)La Réunion 3.103e+00
## factor(ageClass)74.5:factor(reg_name)La Réunion 2.915e+00
## factor(ageClass)84.5:factor(reg_name)La Réunion -1.471e+01
## factor(ageClass)94.5:factor(reg_name)La Réunion -1.536e+01
## factor(ageClass)14.5:factor(reg_name)Martinique 2.559e+00
## factor(ageClass)24.5:factor(reg_name)Martinique 4.083e+00
## factor(ageClass)34.5:factor(reg_name)Martinique 3.588e+00
## factor(ageClass)44.5:factor(reg_name)Martinique 1.977e+00
## factor(ageClass)54.5:factor(reg_name)Martinique 3.713e+00
## factor(ageClass)64.5:factor(reg_name)Martinique 2.931e+00
## factor(ageClass)74.5:factor(reg_name)Martinique 4.360e+00
## factor(ageClass)84.5:factor(reg_name)Martinique -5.597e+00
## factor(ageClass)94.5:factor(reg_name)Martinique 2.864e+00
## factor(ageClass)14.5:factor(reg_name)Mayotte -3.947e+01
## factor(ageClass)24.5:factor(reg_name)Mayotte -4.009e+01
## factor(ageClass)34.5:factor(reg_name)Mayotte -3.980e+01
## factor(ageClass)44.5:factor(reg_name)Mayotte -4.000e+01
## factor(ageClass)54.5:factor(reg_name)Mayotte -4.010e+01
## factor(ageClass)64.5:factor(reg_name)Mayotte -2.478e+01
## factor(ageClass)74.5:factor(reg_name)Mayotte -3.841e+01
## factor(ageClass)84.5:factor(reg_name)Mayotte NA
## factor(ageClass)94.5:factor(reg_name)Mayotte NA
## factor(ageClass)14.5:factor(reg_name)Normandie -4.497e-02
## factor(ageClass)24.5:factor(reg_name)Normandie 1.325e-01
## factor(ageClass)34.5:factor(reg_name)Normandie -2.421e-01
## factor(ageClass)44.5:factor(reg_name)Normandie 1.924e-01
## factor(ageClass)54.5:factor(reg_name)Normandie 1.877e-01
## factor(ageClass)64.5:factor(reg_name)Normandie 3.366e-01
## factor(ageClass)74.5:factor(reg_name)Normandie 8.041e-02
## factor(ageClass)84.5:factor(reg_name)Normandie 1.018e-01
## factor(ageClass)94.5:factor(reg_name)Normandie -4.715e-02
## factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine -1.887e-01
## factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine -2.545e-01
## factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine -3.946e-01
## factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine -1.313e-01
## factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine -3.995e-01
## factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine 1.504e-02
## factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine -4.278e-01
## factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine -4.002e-01
## factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine -8.593e-01
## factor(ageClass)14.5:factor(reg_name)Occitanie -1.324e-01
## factor(ageClass)24.5:factor(reg_name)Occitanie 6.181e-02
## factor(ageClass)34.5:factor(reg_name)Occitanie 1.343e-01
## factor(ageClass)44.5:factor(reg_name)Occitanie 5.576e-02
## factor(ageClass)54.5:factor(reg_name)Occitanie -4.864e-02
## factor(ageClass)64.5:factor(reg_name)Occitanie 1.125e-01
## factor(ageClass)74.5:factor(reg_name)Occitanie 8.985e-02
## factor(ageClass)84.5:factor(reg_name)Occitanie 2.944e-01
## factor(ageClass)94.5:factor(reg_name)Occitanie 4.684e-01
## factor(ageClass)14.5:factor(reg_name)Pays de la Loire -2.459e-03
## factor(ageClass)24.5:factor(reg_name)Pays de la Loire 6.938e-02
## factor(ageClass)34.5:factor(reg_name)Pays de la Loire 1.088e-01
## factor(ageClass)44.5:factor(reg_name)Pays de la Loire 3.059e-01
## factor(ageClass)54.5:factor(reg_name)Pays de la Loire 3.352e-01
## factor(ageClass)64.5:factor(reg_name)Pays de la Loire 4.425e-01
## factor(ageClass)74.5:factor(reg_name)Pays de la Loire 4.095e-01
## factor(ageClass)84.5:factor(reg_name)Pays de la Loire 6.909e-01
## factor(ageClass)94.5:factor(reg_name)Pays de la Loire 7.200e-01
## factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur -2.526e-01
## factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur -1.770e-01
## factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur -9.616e-02
## factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur -1.800e-01
## factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur -6.069e-02
## factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur 1.360e-01
## factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur -4.271e-01
## factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur -2.201e-01
## factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur -2.505e-01
## time:factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté 2.342e-02
## time:factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté -1.631e-02
## time:factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté -6.313e-03
## time:factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté 1.157e-02
## time:factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté 1.391e-02
## time:factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté -2.512e-03
## time:factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté -3.080e-03
## time:factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté -1.621e-02
## time:factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté 2.994e-02
## time:factor(ageClass)14.5:factor(reg_name)Bretagne 2.442e-02
## time:factor(ageClass)24.5:factor(reg_name)Bretagne 5.557e-02
## time:factor(ageClass)34.5:factor(reg_name)Bretagne 1.689e-02
## time:factor(ageClass)44.5:factor(reg_name)Bretagne 9.613e-03
## time:factor(ageClass)54.5:factor(reg_name)Bretagne 1.703e-02
## time:factor(ageClass)64.5:factor(reg_name)Bretagne 1.699e-02
## time:factor(ageClass)74.5:factor(reg_name)Bretagne 6.362e-03
## time:factor(ageClass)84.5:factor(reg_name)Bretagne 4.643e-02
## time:factor(ageClass)94.5:factor(reg_name)Bretagne 5.496e-02
## time:factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire 7.582e-03
## time:factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire -2.590e-02
## time:factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire -3.447e-02
## time:factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire -2.766e-02
## time:factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire -2.116e-02
## time:factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire -3.703e-02
## time:factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire 1.531e-02
## time:factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire -1.176e-02
## time:factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire 2.228e-02
## time:factor(ageClass)14.5:factor(reg_name)Corse 2.007e-01
## time:factor(ageClass)24.5:factor(reg_name)Corse 1.635e-01
## time:factor(ageClass)34.5:factor(reg_name)Corse 2.035e-01
## time:factor(ageClass)44.5:factor(reg_name)Corse 1.010e-01
## time:factor(ageClass)54.5:factor(reg_name)Corse 1.257e-01
## time:factor(ageClass)64.5:factor(reg_name)Corse 1.922e-01
## time:factor(ageClass)74.5:factor(reg_name)Corse 1.818e-01
## time:factor(ageClass)84.5:factor(reg_name)Corse 8.291e-02
## time:factor(ageClass)94.5:factor(reg_name)Corse -6.688e-01
## time:factor(ageClass)14.5:factor(reg_name)Grand Est 3.855e-02
## time:factor(ageClass)24.5:factor(reg_name)Grand Est 1.023e-02
## time:factor(ageClass)34.5:factor(reg_name)Grand Est -5.719e-03
## time:factor(ageClass)44.5:factor(reg_name)Grand Est -2.592e-03
## time:factor(ageClass)54.5:factor(reg_name)Grand Est -1.161e-02
## time:factor(ageClass)64.5:factor(reg_name)Grand Est -8.163e-03
## time:factor(ageClass)74.5:factor(reg_name)Grand Est -6.686e-04
## time:factor(ageClass)84.5:factor(reg_name)Grand Est 2.883e-02
## time:factor(ageClass)94.5:factor(reg_name)Grand Est 2.131e-02
## time:factor(ageClass)14.5:factor(reg_name)Guadeloupe -1.471e+01
## time:factor(ageClass)24.5:factor(reg_name)Guadeloupe -1.471e+01
## time:factor(ageClass)34.5:factor(reg_name)Guadeloupe -1.463e+01
## time:factor(ageClass)44.5:factor(reg_name)Guadeloupe -1.485e+01
## time:factor(ageClass)54.5:factor(reg_name)Guadeloupe -1.483e+01
## time:factor(ageClass)64.5:factor(reg_name)Guadeloupe -1.468e+01
## time:factor(ageClass)74.5:factor(reg_name)Guadeloupe -1.505e+01
## time:factor(ageClass)84.5:factor(reg_name)Guadeloupe -1.487e+01
## time:factor(ageClass)94.5:factor(reg_name)Guadeloupe NA
## time:factor(ageClass)14.5:factor(reg_name)Guyane 4.647e-02
## time:factor(ageClass)24.5:factor(reg_name)Guyane 1.713e-01
## time:factor(ageClass)34.5:factor(reg_name)Guyane 1.380e+01
## time:factor(ageClass)44.5:factor(reg_name)Guyane 1.067e-01
## time:factor(ageClass)54.5:factor(reg_name)Guyane -3.912e-01
## time:factor(ageClass)64.5:factor(reg_name)Guyane 2.184e-02
## time:factor(ageClass)74.5:factor(reg_name)Guyane NA
## time:factor(ageClass)84.5:factor(reg_name)Guyane -3.985e-03
## time:factor(ageClass)94.5:factor(reg_name)Guyane NA
## time:factor(ageClass)14.5:factor(reg_name)Hauts-de-France 3.784e-02
## time:factor(ageClass)24.5:factor(reg_name)Hauts-de-France 9.383e-03
## time:factor(ageClass)34.5:factor(reg_name)Hauts-de-France -6.677e-04
## time:factor(ageClass)44.5:factor(reg_name)Hauts-de-France 3.555e-03
## time:factor(ageClass)54.5:factor(reg_name)Hauts-de-France 5.038e-03
## time:factor(ageClass)64.5:factor(reg_name)Hauts-de-France -1.350e-02
## time:factor(ageClass)74.5:factor(reg_name)Hauts-de-France -1.529e-02
## time:factor(ageClass)84.5:factor(reg_name)Hauts-de-France -1.678e-03
## time:factor(ageClass)94.5:factor(reg_name)Hauts-de-France 2.214e-02
## time:factor(ageClass)14.5:factor(reg_name)ÃŽle-de-France 7.865e-03
## time:factor(ageClass)24.5:factor(reg_name)ÃŽle-de-France 1.240e-02
## time:factor(ageClass)34.5:factor(reg_name)ÃŽle-de-France -5.554e-03
## time:factor(ageClass)44.5:factor(reg_name)ÃŽle-de-France -7.092e-03
## time:factor(ageClass)54.5:factor(reg_name)ÃŽle-de-France -7.372e-03
## time:factor(ageClass)64.5:factor(reg_name)ÃŽle-de-France -1.357e-02
## time:factor(ageClass)74.5:factor(reg_name)ÃŽle-de-France -6.839e-04
## time:factor(ageClass)84.5:factor(reg_name)ÃŽle-de-France 4.661e-02
## time:factor(ageClass)94.5:factor(reg_name)ÃŽle-de-France 3.542e-02
## time:factor(ageClass)14.5:factor(reg_name)La Réunion -7.867e-02
## time:factor(ageClass)24.5:factor(reg_name)La Réunion 8.907e-02
## time:factor(ageClass)34.5:factor(reg_name)La Réunion -1.188e-01
## time:factor(ageClass)44.5:factor(reg_name)La Réunion -1.240e-01
## time:factor(ageClass)54.5:factor(reg_name)La Réunion -1.187e-01
## time:factor(ageClass)64.5:factor(reg_name)La Réunion -2.292e-01
## time:factor(ageClass)74.5:factor(reg_name)La Réunion -6.062e-01
## time:factor(ageClass)84.5:factor(reg_name)La Réunion -1.363e-01
## time:factor(ageClass)94.5:factor(reg_name)La Réunion NA
## time:factor(ageClass)14.5:factor(reg_name)Martinique -1.595e-01
## time:factor(ageClass)24.5:factor(reg_name)Martinique -2.394e-01
## time:factor(ageClass)34.5:factor(reg_name)Martinique -2.756e-01
## time:factor(ageClass)44.5:factor(reg_name)Martinique -5.708e-02
## time:factor(ageClass)54.5:factor(reg_name)Martinique -2.884e-01
## time:factor(ageClass)64.5:factor(reg_name)Martinique -2.394e-01
## time:factor(ageClass)74.5:factor(reg_name)Martinique -4.780e-01
## time:factor(ageClass)84.5:factor(reg_name)Martinique 2.186e+00
## time:factor(ageClass)94.5:factor(reg_name)Martinique -1.919e-01
## time:factor(ageClass)14.5:factor(reg_name)Mayotte 1.163e-01
## time:factor(ageClass)24.5:factor(reg_name)Mayotte 1.284e-01
## time:factor(ageClass)34.5:factor(reg_name)Mayotte 6.187e-02
## time:factor(ageClass)44.5:factor(reg_name)Mayotte 8.733e-02
## time:factor(ageClass)54.5:factor(reg_name)Mayotte 1.289e-01
## time:factor(ageClass)64.5:factor(reg_name)Mayotte 2.115e-02
## time:factor(ageClass)74.5:factor(reg_name)Mayotte 4.768e-02
## time:factor(ageClass)84.5:factor(reg_name)Mayotte NA
## time:factor(ageClass)94.5:factor(reg_name)Mayotte NA
## time:factor(ageClass)14.5:factor(reg_name)Normandie 3.327e-02
## time:factor(ageClass)24.5:factor(reg_name)Normandie 1.468e-02
## time:factor(ageClass)34.5:factor(reg_name)Normandie 4.344e-02
## time:factor(ageClass)44.5:factor(reg_name)Normandie 1.516e-02
## time:factor(ageClass)54.5:factor(reg_name)Normandie 1.055e-02
## time:factor(ageClass)64.5:factor(reg_name)Normandie -2.129e-02
## time:factor(ageClass)74.5:factor(reg_name)Normandie 1.395e-02
## time:factor(ageClass)84.5:factor(reg_name)Normandie 4.524e-02
## time:factor(ageClass)94.5:factor(reg_name)Normandie 5.840e-02
## time:factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine 4.397e-02
## time:factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine 3.781e-02
## time:factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine 3.038e-02
## time:factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine 2.019e-02
## time:factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine 3.983e-02
## time:factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine -2.297e-04
## time:factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine 2.283e-02
## time:factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine 4.758e-02
## time:factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine 4.579e-02
## time:factor(ageClass)14.5:factor(reg_name)Occitanie 9.375e-03
## time:factor(ageClass)24.5:factor(reg_name)Occitanie -1.093e-02
## time:factor(ageClass)34.5:factor(reg_name)Occitanie -1.130e-02
## time:factor(ageClass)44.5:factor(reg_name)Occitanie -1.081e-02
## time:factor(ageClass)54.5:factor(reg_name)Occitanie 1.084e-03
## time:factor(ageClass)64.5:factor(reg_name)Occitanie -2.105e-02
## time:factor(ageClass)74.5:factor(reg_name)Occitanie -1.978e-02
## time:factor(ageClass)84.5:factor(reg_name)Occitanie -9.939e-03
## time:factor(ageClass)94.5:factor(reg_name)Occitanie -3.939e-02
## time:factor(ageClass)14.5:factor(reg_name)Pays de la Loire 1.146e-02
## time:factor(ageClass)24.5:factor(reg_name)Pays de la Loire 1.086e-02
## time:factor(ageClass)34.5:factor(reg_name)Pays de la Loire 3.081e-04
## time:factor(ageClass)44.5:factor(reg_name)Pays de la Loire -1.713e-02
## time:factor(ageClass)54.5:factor(reg_name)Pays de la Loire -1.275e-02
## time:factor(ageClass)64.5:factor(reg_name)Pays de la Loire -3.097e-02
## time:factor(ageClass)74.5:factor(reg_name)Pays de la Loire -1.852e-02
## time:factor(ageClass)84.5:factor(reg_name)Pays de la Loire -2.788e-02
## time:factor(ageClass)94.5:factor(reg_name)Pays de la Loire -5.074e-02
## time:factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur 2.839e-02
## time:factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur 9.332e-03
## time:factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur 4.271e-04
## time:factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur 1.097e-02
## time:factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur 9.327e-03
## time:factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur -5.555e-03
## time:factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur 2.321e-02
## time:factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur 4.253e-02
## time:factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur 3.943e-02
## Std. Error
## (Intercept) 4.188e-02
## time 4.169e-03
## factor(ageClass)14.5 4.862e-02
## factor(ageClass)24.5 4.822e-02
## factor(ageClass)34.5 4.793e-02
## factor(ageClass)44.5 4.804e-02
## factor(ageClass)54.5 4.816e-02
## factor(ageClass)64.5 5.157e-02
## factor(ageClass)74.5 5.467e-02
## factor(ageClass)84.5 6.083e-02
## factor(ageClass)94.5 7.670e-02
## factor(reg_name)Bourgogne-Franche-Comté 9.611e-02
## factor(reg_name)Bretagne 8.841e-02
## factor(reg_name)Centre-Val de Loire 1.075e-01
## factor(reg_name)Corse 4.850e-01
## factor(reg_name)Grand Est 6.602e-02
## factor(reg_name)Guadeloupe 6.537e+03
## factor(reg_name)Guyane 3.327e+03
## factor(reg_name)Hauts-de-France 5.497e-02
## factor(reg_name)ÃŽle-de-France 5.209e-02
## factor(reg_name)La Réunion 4.602e-01
## factor(reg_name)Martinique 1.599e+00
## factor(reg_name)Mayotte 1.378e+04
## factor(reg_name)Normandie 8.338e-02
## factor(reg_name)Nouvelle-Aquitaine 7.924e-02
## factor(reg_name)Occitanie 7.267e-02
## factor(reg_name)Pays de la Loire 8.094e-02
## factor(reg_name)Provence-Alpes-Côte d'Azur 6.378e-02
## time:factor(ageClass)14.5 4.861e-03
## time:factor(ageClass)24.5 4.795e-03
## time:factor(ageClass)34.5 4.793e-03
## time:factor(ageClass)44.5 4.807e-03
## time:factor(ageClass)54.5 4.827e-03
## time:factor(ageClass)64.5 5.154e-03
## time:factor(ageClass)74.5 5.479e-03
## time:factor(ageClass)84.5 6.146e-03
## time:factor(ageClass)94.5 8.022e-03
## time:factor(reg_name)Bourgogne-Franche-Comté 9.787e-03
## time:factor(reg_name)Bretagne 9.381e-03
## time:factor(reg_name)Centre-Val de Loire 1.065e-02
## time:factor(reg_name)Corse 4.109e-02
## time:factor(reg_name)Grand Est 6.537e-03
## time:factor(reg_name)Guadeloupe 5.943e+02
## time:factor(reg_name)Guyane 3.048e+02
## time:factor(reg_name)Hauts-de-France 5.470e-03
## time:factor(reg_name)ÃŽle-de-France 5.172e-03
## time:factor(reg_name)La Réunion 3.859e-02
## time:factor(reg_name)Martinique 1.471e-01
## time:factor(reg_name)Mayotte 1.233e+03
## time:factor(reg_name)Normandie 8.319e-03
## time:factor(reg_name)Nouvelle-Aquitaine 7.760e-03
## time:factor(reg_name)Occitanie 7.125e-03
## time:factor(reg_name)Pays de la Loire 7.968e-03
## time:factor(reg_name)Provence-Alpes-Côte d'Azur 6.596e-03
## factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté 1.101e-01
## factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté 1.087e-01
## factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté 1.092e-01
## factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté 1.087e-01
## factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté 1.091e-01
## factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté 1.130e-01
## factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté 1.201e-01
## factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté 1.293e-01
## factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté 1.584e-01
## factor(ageClass)14.5:factor(reg_name)Bretagne 1.030e-01
## factor(ageClass)24.5:factor(reg_name)Bretagne 1.010e-01
## factor(ageClass)34.5:factor(reg_name)Bretagne 1.033e-01
## factor(ageClass)44.5:factor(reg_name)Bretagne 1.024e-01
## factor(ageClass)54.5:factor(reg_name)Bretagne 1.035e-01
## factor(ageClass)64.5:factor(reg_name)Bretagne 1.137e-01
## factor(ageClass)74.5:factor(reg_name)Bretagne 1.238e-01
## factor(ageClass)84.5:factor(reg_name)Bretagne 1.257e-01
## factor(ageClass)94.5:factor(reg_name)Bretagne 1.535e-01
## factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire 1.220e-01
## factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire 1.207e-01
## factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire 1.207e-01
## factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire 1.199e-01
## factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire 1.211e-01
## factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire 1.244e-01
## factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire 1.337e-01
## factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire 1.393e-01
## factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire 1.624e-01
## factor(ageClass)14.5:factor(reg_name)Corse 5.266e-01
## factor(ageClass)24.5:factor(reg_name)Corse 5.178e-01
## factor(ageClass)34.5:factor(reg_name)Corse 5.031e-01
## factor(ageClass)44.5:factor(reg_name)Corse 5.154e-01
## factor(ageClass)54.5:factor(reg_name)Corse 5.107e-01
## factor(ageClass)64.5:factor(reg_name)Corse 5.109e-01
## factor(ageClass)74.5:factor(reg_name)Corse 5.313e-01
## factor(ageClass)84.5:factor(reg_name)Corse 5.665e-01
## factor(ageClass)94.5:factor(reg_name)Corse 6.615e+00
## factor(ageClass)14.5:factor(reg_name)Grand Est 7.725e-02
## factor(ageClass)24.5:factor(reg_name)Grand Est 7.626e-02
## factor(ageClass)34.5:factor(reg_name)Grand Est 7.617e-02
## factor(ageClass)44.5:factor(reg_name)Grand Est 7.653e-02
## factor(ageClass)54.5:factor(reg_name)Grand Est 7.713e-02
## factor(ageClass)64.5:factor(reg_name)Grand Est 8.261e-02
## factor(ageClass)74.5:factor(reg_name)Grand Est 9.014e-02
## factor(ageClass)84.5:factor(reg_name)Grand Est 9.890e-02
## factor(ageClass)94.5:factor(reg_name)Grand Est 1.270e-01
## factor(ageClass)14.5:factor(reg_name)Guadeloupe 6.537e+03
## factor(ageClass)24.5:factor(reg_name)Guadeloupe 6.537e+03
## factor(ageClass)34.5:factor(reg_name)Guadeloupe 6.537e+03
## factor(ageClass)44.5:factor(reg_name)Guadeloupe 6.537e+03
## factor(ageClass)54.5:factor(reg_name)Guadeloupe 6.537e+03
## factor(ageClass)64.5:factor(reg_name)Guadeloupe 6.537e+03
## factor(ageClass)74.5:factor(reg_name)Guadeloupe 6.537e+03
## factor(ageClass)84.5:factor(reg_name)Guadeloupe 7.180e+03
## factor(ageClass)94.5:factor(reg_name)Guadeloupe NA
## factor(ageClass)14.5:factor(reg_name)Guyane 3.900e+03
## factor(ageClass)24.5:factor(reg_name)Guyane 3.327e+03
## factor(ageClass)34.5:factor(reg_name)Guyane 3.754e+03
## factor(ageClass)44.5:factor(reg_name)Guyane 3.327e+03
## factor(ageClass)54.5:factor(reg_name)Guyane 3.327e+03
## factor(ageClass)64.5:factor(reg_name)Guyane 5.174e+03
## factor(ageClass)74.5:factor(reg_name)Guyane NA
## factor(ageClass)84.5:factor(reg_name)Guyane 5.775e+03
## factor(ageClass)94.5:factor(reg_name)Guyane NA
## factor(ageClass)14.5:factor(reg_name)Hauts-de-France 6.385e-02
## factor(ageClass)24.5:factor(reg_name)Hauts-de-France 6.353e-02
## factor(ageClass)34.5:factor(reg_name)Hauts-de-France 6.304e-02
## factor(ageClass)44.5:factor(reg_name)Hauts-de-France 6.300e-02
## factor(ageClass)54.5:factor(reg_name)Hauts-de-France 6.354e-02
## factor(ageClass)64.5:factor(reg_name)Hauts-de-France 6.769e-02
## factor(ageClass)74.5:factor(reg_name)Hauts-de-France 7.246e-02
## factor(ageClass)84.5:factor(reg_name)Hauts-de-France 7.972e-02
## factor(ageClass)94.5:factor(reg_name)Hauts-de-France 1.026e-01
## factor(ageClass)14.5:factor(reg_name)ÃŽle-de-France 6.053e-02
## factor(ageClass)24.5:factor(reg_name)ÃŽle-de-France 5.939e-02
## factor(ageClass)34.5:factor(reg_name)ÃŽle-de-France 5.916e-02
## factor(ageClass)44.5:factor(reg_name)ÃŽle-de-France 5.930e-02
## factor(ageClass)54.5:factor(reg_name)ÃŽle-de-France 5.976e-02
## factor(ageClass)64.5:factor(reg_name)ÃŽle-de-France 6.343e-02
## factor(ageClass)74.5:factor(reg_name)ÃŽle-de-France 6.883e-02
## factor(ageClass)84.5:factor(reg_name)ÃŽle-de-France 7.657e-02
## factor(ageClass)94.5:factor(reg_name)ÃŽle-de-France 9.804e-02
## factor(ageClass)14.5:factor(reg_name)La Réunion 5.143e-01
## factor(ageClass)24.5:factor(reg_name)La Réunion 6.712e-01
## factor(ageClass)34.5:factor(reg_name)La Réunion 5.019e-01
## factor(ageClass)44.5:factor(reg_name)La Réunion 5.050e-01
## factor(ageClass)54.5:factor(reg_name)La Réunion 5.076e-01
## factor(ageClass)64.5:factor(reg_name)La Réunion 5.180e-01
## factor(ageClass)74.5:factor(reg_name)La Réunion 7.780e-01
## factor(ageClass)84.5:factor(reg_name)La Réunion 2.192e+03
## factor(ageClass)94.5:factor(reg_name)La Réunion 6.523e+03
## factor(ageClass)14.5:factor(reg_name)Martinique 1.674e+00
## factor(ageClass)24.5:factor(reg_name)Martinique 1.640e+00
## factor(ageClass)34.5:factor(reg_name)Martinique 1.639e+00
## factor(ageClass)44.5:factor(reg_name)Martinique 1.645e+00
## factor(ageClass)54.5:factor(reg_name)Martinique 1.625e+00
## factor(ageClass)64.5:factor(reg_name)Martinique 1.648e+00
## factor(ageClass)74.5:factor(reg_name)Martinique 1.690e+00
## factor(ageClass)84.5:factor(reg_name)Martinique 4.703e+00
## factor(ageClass)94.5:factor(reg_name)Martinique 1.883e+00
## factor(ageClass)14.5:factor(reg_name)Mayotte 1.402e+04
## factor(ageClass)24.5:factor(reg_name)Mayotte 1.390e+04
## factor(ageClass)34.5:factor(reg_name)Mayotte 1.392e+04
## factor(ageClass)44.5:factor(reg_name)Mayotte 1.393e+04
## factor(ageClass)54.5:factor(reg_name)Mayotte 1.393e+04
## factor(ageClass)64.5:factor(reg_name)Mayotte 1.378e+04
## factor(ageClass)74.5:factor(reg_name)Mayotte 1.405e+04
## factor(ageClass)84.5:factor(reg_name)Mayotte NA
## factor(ageClass)94.5:factor(reg_name)Mayotte NA
## factor(ageClass)14.5:factor(reg_name)Normandie 9.595e-02
## factor(ageClass)24.5:factor(reg_name)Normandie 9.687e-02
## factor(ageClass)34.5:factor(reg_name)Normandie 9.626e-02
## factor(ageClass)44.5:factor(reg_name)Normandie 9.539e-02
## factor(ageClass)54.5:factor(reg_name)Normandie 9.609e-02
## factor(ageClass)64.5:factor(reg_name)Normandie 1.004e-01
## factor(ageClass)74.5:factor(reg_name)Normandie 1.082e-01
## factor(ageClass)84.5:factor(reg_name)Normandie 1.193e-01
## factor(ageClass)94.5:factor(reg_name)Normandie 1.582e-01
## factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine 9.167e-02
## factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine 9.026e-02
## factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine 9.064e-02
## factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine 9.032e-02
## factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine 9.131e-02
## factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine 9.584e-02
## factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine 1.044e-01
## factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine 1.126e-01
## factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine 1.470e-01
## factor(ageClass)14.5:factor(reg_name)Occitanie 8.296e-02
## factor(ageClass)24.5:factor(reg_name)Occitanie 8.174e-02
## factor(ageClass)34.5:factor(reg_name)Occitanie 8.169e-02
## factor(ageClass)44.5:factor(reg_name)Occitanie 8.179e-02
## factor(ageClass)54.5:factor(reg_name)Occitanie 8.190e-02
## factor(ageClass)64.5:factor(reg_name)Occitanie 8.624e-02
## factor(ageClass)74.5:factor(reg_name)Occitanie 9.095e-02
## factor(ageClass)84.5:factor(reg_name)Occitanie 9.567e-02
## factor(ageClass)94.5:factor(reg_name)Occitanie 1.111e-01
## factor(ageClass)14.5:factor(reg_name)Pays de la Loire 9.212e-02
## factor(ageClass)24.5:factor(reg_name)Pays de la Loire 9.173e-02
## factor(ageClass)34.5:factor(reg_name)Pays de la Loire 9.237e-02
## factor(ageClass)44.5:factor(reg_name)Pays de la Loire 9.183e-02
## factor(ageClass)54.5:factor(reg_name)Pays de la Loire 9.241e-02
## factor(ageClass)64.5:factor(reg_name)Pays de la Loire 9.785e-02
## factor(ageClass)74.5:factor(reg_name)Pays de la Loire 1.050e-01
## factor(ageClass)84.5:factor(reg_name)Pays de la Loire 1.116e-01
## factor(ageClass)94.5:factor(reg_name)Pays de la Loire 1.335e-01
## factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur 7.281e-02
## factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur 7.217e-02
## factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur 7.161e-02
## factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur 7.146e-02
## factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur 7.172e-02
## factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur 7.535e-02
## factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur 7.969e-02
## factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur 8.629e-02
## factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur 1.038e-01
## time:factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté 1.108e-02
## time:factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté 1.097e-02
## time:factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté 1.106e-02
## time:factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté 1.104e-02
## time:factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté 1.102e-02
## time:factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté 1.144e-02
## time:factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté 1.208e-02
## time:factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté 1.322e-02
## time:factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté 1.667e-02
## time:factor(ageClass)14.5:factor(reg_name)Bretagne 1.073e-02
## time:factor(ageClass)24.5:factor(reg_name)Bretagne 1.068e-02
## time:factor(ageClass)34.5:factor(reg_name)Bretagne 1.092e-02
## time:factor(ageClass)44.5:factor(reg_name)Bretagne 1.085e-02
## time:factor(ageClass)54.5:factor(reg_name)Bretagne 1.095e-02
## time:factor(ageClass)64.5:factor(reg_name)Bretagne 1.189e-02
## time:factor(ageClass)74.5:factor(reg_name)Bretagne 1.279e-02
## time:factor(ageClass)84.5:factor(reg_name)Bretagne 1.363e-02
## time:factor(ageClass)94.5:factor(reg_name)Bretagne 1.696e-02
## time:factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire 1.205e-02
## time:factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire 1.192e-02
## time:factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire 1.192e-02
## time:factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire 1.187e-02
## time:factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire 1.196e-02
## time:factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire 1.226e-02
## time:factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire 1.314e-02
## time:factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire 1.380e-02
## time:factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire 1.631e-02
## time:factor(ageClass)14.5:factor(reg_name)Corse 4.563e-02
## time:factor(ageClass)24.5:factor(reg_name)Corse 4.429e-02
## time:factor(ageClass)34.5:factor(reg_name)Corse 4.365e-02
## time:factor(ageClass)44.5:factor(reg_name)Corse 4.470e-02
## time:factor(ageClass)54.5:factor(reg_name)Corse 4.426e-02
## time:factor(ageClass)64.5:factor(reg_name)Corse 4.478e-02
## time:factor(ageClass)74.5:factor(reg_name)Corse 4.749e-02
## time:factor(ageClass)84.5:factor(reg_name)Corse 4.855e-02
## time:factor(ageClass)94.5:factor(reg_name)Corse 4.163e-01
## time:factor(ageClass)14.5:factor(reg_name)Grand Est 7.640e-03
## time:factor(ageClass)24.5:factor(reg_name)Grand Est 7.533e-03
## time:factor(ageClass)34.5:factor(reg_name)Grand Est 7.527e-03
## time:factor(ageClass)44.5:factor(reg_name)Grand Est 7.561e-03
## time:factor(ageClass)54.5:factor(reg_name)Grand Est 7.620e-03
## time:factor(ageClass)64.5:factor(reg_name)Grand Est 8.116e-03
## time:factor(ageClass)74.5:factor(reg_name)Grand Est 8.814e-03
## time:factor(ageClass)84.5:factor(reg_name)Grand Est 9.742e-03
## time:factor(ageClass)94.5:factor(reg_name)Grand Est 1.276e-02
## time:factor(ageClass)14.5:factor(reg_name)Guadeloupe 5.943e+02
## time:factor(ageClass)24.5:factor(reg_name)Guadeloupe 5.943e+02
## time:factor(ageClass)34.5:factor(reg_name)Guadeloupe 5.943e+02
## time:factor(ageClass)44.5:factor(reg_name)Guadeloupe 5.943e+02
## time:factor(ageClass)54.5:factor(reg_name)Guadeloupe 5.943e+02
## time:factor(ageClass)64.5:factor(reg_name)Guadeloupe 5.943e+02
## time:factor(ageClass)74.5:factor(reg_name)Guadeloupe 5.943e+02
## time:factor(ageClass)84.5:factor(reg_name)Guadeloupe 6.632e+02
## time:factor(ageClass)94.5:factor(reg_name)Guadeloupe NA
## time:factor(ageClass)14.5:factor(reg_name)Guyane 3.636e+02
## time:factor(ageClass)24.5:factor(reg_name)Guyane 3.048e+02
## time:factor(ageClass)34.5:factor(reg_name)Guyane 4.626e+02
## time:factor(ageClass)44.5:factor(reg_name)Guyane 3.048e+02
## time:factor(ageClass)54.5:factor(reg_name)Guyane 3.048e+02
## time:factor(ageClass)64.5:factor(reg_name)Guyane 1.162e+03
## time:factor(ageClass)74.5:factor(reg_name)Guyane NA
## time:factor(ageClass)84.5:factor(reg_name)Guyane 1.589e+03
## time:factor(ageClass)94.5:factor(reg_name)Guyane NA
## time:factor(ageClass)14.5:factor(reg_name)Hauts-de-France 6.392e-03
## time:factor(ageClass)24.5:factor(reg_name)Hauts-de-France 6.328e-03
## time:factor(ageClass)34.5:factor(reg_name)Hauts-de-France 6.302e-03
## time:factor(ageClass)44.5:factor(reg_name)Hauts-de-France 6.305e-03
## time:factor(ageClass)54.5:factor(reg_name)Hauts-de-France 6.370e-03
## time:factor(ageClass)64.5:factor(reg_name)Hauts-de-France 6.754e-03
## time:factor(ageClass)74.5:factor(reg_name)Hauts-de-France 7.231e-03
## time:factor(ageClass)84.5:factor(reg_name)Hauts-de-France 8.052e-03
## time:factor(ageClass)94.5:factor(reg_name)Hauts-de-France 1.067e-02
## time:factor(ageClass)14.5:factor(reg_name)ÃŽle-de-France 6.021e-03
## time:factor(ageClass)24.5:factor(reg_name)ÃŽle-de-France 5.896e-03
## time:factor(ageClass)34.5:factor(reg_name)ÃŽle-de-France 5.893e-03
## time:factor(ageClass)44.5:factor(reg_name)ÃŽle-de-France 5.913e-03
## time:factor(ageClass)54.5:factor(reg_name)ÃŽle-de-France 5.963e-03
## time:factor(ageClass)64.5:factor(reg_name)ÃŽle-de-France 6.319e-03
## time:factor(ageClass)74.5:factor(reg_name)ÃŽle-de-France 6.881e-03
## time:factor(ageClass)84.5:factor(reg_name)ÃŽle-de-France 7.722e-03
## time:factor(ageClass)94.5:factor(reg_name)ÃŽle-de-France 1.014e-02
## time:factor(ageClass)14.5:factor(reg_name)La Réunion 4.412e-02
## time:factor(ageClass)24.5:factor(reg_name)La Réunion 5.245e-02
## time:factor(ageClass)34.5:factor(reg_name)La Réunion 4.313e-02
## time:factor(ageClass)44.5:factor(reg_name)La Réunion 4.419e-02
## time:factor(ageClass)54.5:factor(reg_name)La Réunion 4.375e-02
## time:factor(ageClass)64.5:factor(reg_name)La Réunion 4.597e-02
## time:factor(ageClass)74.5:factor(reg_name)La Réunion 1.700e-01
## time:factor(ageClass)84.5:factor(reg_name)La Réunion 2.114e+02
## time:factor(ageClass)94.5:factor(reg_name)La Réunion NA
## time:factor(ageClass)14.5:factor(reg_name)Martinique 1.591e-01
## time:factor(ageClass)24.5:factor(reg_name)Martinique 1.522e-01
## time:factor(ageClass)34.5:factor(reg_name)Martinique 1.511e-01
## time:factor(ageClass)44.5:factor(reg_name)Martinique 1.542e-01
## time:factor(ageClass)54.5:factor(reg_name)Martinique 1.498e-01
## time:factor(ageClass)64.5:factor(reg_name)Martinique 1.517e-01
## time:factor(ageClass)74.5:factor(reg_name)Martinique 1.618e-01
## time:factor(ageClass)84.5:factor(reg_name)Martinique 1.284e+00
## time:factor(ageClass)94.5:factor(reg_name)Martinique 1.712e-01
## time:factor(ageClass)14.5:factor(reg_name)Mayotte 1.276e+03
## time:factor(ageClass)24.5:factor(reg_name)Mayotte 1.248e+03
## time:factor(ageClass)34.5:factor(reg_name)Mayotte 1.249e+03
## time:factor(ageClass)44.5:factor(reg_name)Mayotte 1.253e+03
## time:factor(ageClass)54.5:factor(reg_name)Mayotte 1.255e+03
## time:factor(ageClass)64.5:factor(reg_name)Mayotte 1.233e+03
## time:factor(ageClass)74.5:factor(reg_name)Mayotte 1.278e+03
## time:factor(ageClass)84.5:factor(reg_name)Mayotte NA
## time:factor(ageClass)94.5:factor(reg_name)Mayotte NA
## time:factor(ageClass)14.5:factor(reg_name)Normandie 9.619e-03
## time:factor(ageClass)24.5:factor(reg_name)Normandie 9.635e-03
## time:factor(ageClass)34.5:factor(reg_name)Normandie 9.663e-03
## time:factor(ageClass)44.5:factor(reg_name)Normandie 9.552e-03
## time:factor(ageClass)54.5:factor(reg_name)Normandie 9.574e-03
## time:factor(ageClass)64.5:factor(reg_name)Normandie 9.969e-03
## time:factor(ageClass)74.5:factor(reg_name)Normandie 1.070e-02
## time:factor(ageClass)84.5:factor(reg_name)Normandie 1.180e-02
## time:factor(ageClass)94.5:factor(reg_name)Normandie 1.554e-02
## time:factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine 9.040e-03
## time:factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine 8.902e-03
## time:factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine 8.968e-03
## time:factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine 8.948e-03
## time:factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine 9.019e-03
## time:factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine 9.423e-03
## time:factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine 1.033e-02
## time:factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine 1.126e-02
## time:factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine 1.487e-02
## time:factor(ageClass)14.5:factor(reg_name)Occitanie 8.163e-03
## time:factor(ageClass)24.5:factor(reg_name)Occitanie 8.056e-03
## time:factor(ageClass)34.5:factor(reg_name)Occitanie 8.086e-03
## time:factor(ageClass)44.5:factor(reg_name)Occitanie 8.091e-03
## time:factor(ageClass)54.5:factor(reg_name)Occitanie 8.122e-03
## time:factor(ageClass)64.5:factor(reg_name)Occitanie 8.553e-03
## time:factor(ageClass)74.5:factor(reg_name)Occitanie 9.048e-03
## time:factor(ageClass)84.5:factor(reg_name)Occitanie 9.655e-03
## time:factor(ageClass)94.5:factor(reg_name)Occitanie 1.182e-02
## time:factor(ageClass)14.5:factor(reg_name)Pays de la Loire 9.074e-03
## time:factor(ageClass)24.5:factor(reg_name)Pays de la Loire 9.056e-03
## time:factor(ageClass)34.5:factor(reg_name)Pays de la Loire 9.151e-03
## time:factor(ageClass)44.5:factor(reg_name)Pays de la Loire 9.102e-03
## time:factor(ageClass)54.5:factor(reg_name)Pays de la Loire 9.164e-03
## time:factor(ageClass)64.5:factor(reg_name)Pays de la Loire 9.666e-03
## time:factor(ageClass)74.5:factor(reg_name)Pays de la Loire 1.045e-02
## time:factor(ageClass)84.5:factor(reg_name)Pays de la Loire 1.119e-02
## time:factor(ageClass)94.5:factor(reg_name)Pays de la Loire 1.415e-02
## time:factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur 7.548e-03
## time:factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur 7.436e-03
## time:factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur 7.417e-03
## time:factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur 7.398e-03
## time:factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur 7.427e-03
## time:factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur 7.777e-03
## time:factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur 8.217e-03
## time:factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur 8.993e-03
## time:factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur 1.106e-02
## z value
## (Intercept) -4.022
## time 12.340
## factor(ageClass)14.5 -0.108
## factor(ageClass)24.5 -4.166
## factor(ageClass)34.5 -3.678
## factor(ageClass)44.5 -4.329
## factor(ageClass)54.5 -6.784
## factor(ageClass)64.5 -10.830
## factor(ageClass)74.5 -12.264
## factor(ageClass)84.5 -15.916
## factor(ageClass)94.5 -14.693
## factor(reg_name)Bourgogne-Franche-Comté -5.526
## factor(reg_name)Bretagne 7.300
## factor(reg_name)Centre-Val de Loire -0.225
## factor(reg_name)Corse 5.729
## factor(reg_name)Grand Est -10.009
## factor(reg_name)Guadeloupe -0.025
## factor(reg_name)Guyane -0.006
## factor(reg_name)Hauts-de-France 8.754
## factor(reg_name)ÃŽle-de-France 11.175
## factor(reg_name)La Réunion -6.985
## factor(reg_name)Martinique -1.710
## factor(reg_name)Mayotte 0.001
## factor(reg_name)Normandie -1.354
## factor(reg_name)Nouvelle-Aquitaine 2.717
## factor(reg_name)Occitanie 3.694
## factor(reg_name)Pays de la Loire -2.764
## factor(reg_name)Provence-Alpes-Côte d'Azur 7.296
## time:factor(ageClass)14.5 -2.732
## time:factor(ageClass)24.5 0.543
## time:factor(ageClass)34.5 1.555
## time:factor(ageClass)44.5 1.569
## time:factor(ageClass)54.5 1.843
## time:factor(ageClass)64.5 4.110
## time:factor(ageClass)74.5 4.043
## time:factor(ageClass)84.5 0.648
## time:factor(ageClass)94.5 -0.260
## time:factor(reg_name)Bourgogne-Franche-Comté 0.636
## time:factor(reg_name)Bretagne -2.575
## time:factor(reg_name)Centre-Val de Loire 1.604
## time:factor(reg_name)Corse -4.273
## time:factor(reg_name)Grand Est -0.293
## time:factor(reg_name)Guadeloupe 0.025
## time:factor(reg_name)Guyane 0.000
## time:factor(reg_name)Hauts-de-France -2.901
## time:factor(reg_name)ÃŽle-de-France -4.164
## time:factor(reg_name)La Réunion 0.702
## time:factor(reg_name)Martinique 1.541
## time:factor(reg_name)Mayotte 0.000
## time:factor(reg_name)Normandie 0.033
## time:factor(reg_name)Nouvelle-Aquitaine -2.983
## time:factor(reg_name)Occitanie 0.972
## time:factor(reg_name)Pays de la Loire 0.318
## time:factor(reg_name)Provence-Alpes-Côte d'Azur 0.606
## factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté -1.624
## factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté 1.830
## factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté 0.376
## factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté -0.828
## factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté -1.048
## factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté 0.989
## factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté 1.269
## factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté 1.861
## factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté 0.456
## factor(ageClass)14.5:factor(reg_name)Bretagne -1.889
## factor(ageClass)24.5:factor(reg_name)Bretagne -2.681
## factor(ageClass)34.5:factor(reg_name)Bretagne -1.944
## factor(ageClass)44.5:factor(reg_name)Bretagne 0.420
## factor(ageClass)54.5:factor(reg_name)Bretagne 0.392
## factor(ageClass)64.5:factor(reg_name)Bretagne -0.992
## factor(ageClass)74.5:factor(reg_name)Bretagne 1.109
## factor(ageClass)84.5:factor(reg_name)Bretagne 0.494
## factor(ageClass)94.5:factor(reg_name)Bretagne 0.871
## factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire -0.030
## factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire 0.603
## factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire 1.516
## factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire 1.680
## factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire 1.279
## factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire 2.370
## factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire -0.903
## factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire 1.515
## factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire 0.259
## factor(ageClass)14.5:factor(reg_name)Corse -4.732
## factor(ageClass)24.5:factor(reg_name)Corse -3.671
## factor(ageClass)34.5:factor(reg_name)Corse -4.373
## factor(ageClass)44.5:factor(reg_name)Corse -2.764
## factor(ageClass)54.5:factor(reg_name)Corse -2.549
## factor(ageClass)64.5:factor(reg_name)Corse -3.153
## factor(ageClass)74.5:factor(reg_name)Corse -2.987
## factor(ageClass)84.5:factor(reg_name)Corse -1.017
## factor(ageClass)94.5:factor(reg_name)Corse 1.976
## factor(ageClass)14.5:factor(reg_name)Grand Est -3.651
## factor(ageClass)24.5:factor(reg_name)Grand Est 2.590
## factor(ageClass)34.5:factor(reg_name)Grand Est 2.487
## factor(ageClass)44.5:factor(reg_name)Grand Est 2.680
## factor(ageClass)54.5:factor(reg_name)Grand Est 3.744
## factor(ageClass)64.5:factor(reg_name)Grand Est 5.212
## factor(ageClass)74.5:factor(reg_name)Grand Est 1.989
## factor(ageClass)84.5:factor(reg_name)Grand Est 2.142
## factor(ageClass)94.5:factor(reg_name)Grand Est 2.608
## factor(ageClass)14.5:factor(reg_name)Guadeloupe 0.025
## factor(ageClass)24.5:factor(reg_name)Guadeloupe 0.025
## factor(ageClass)34.5:factor(reg_name)Guadeloupe 0.025
## factor(ageClass)44.5:factor(reg_name)Guadeloupe 0.025
## factor(ageClass)54.5:factor(reg_name)Guadeloupe 0.025
## factor(ageClass)64.5:factor(reg_name)Guadeloupe 0.025
## factor(ageClass)74.5:factor(reg_name)Guadeloupe 0.025
## factor(ageClass)84.5:factor(reg_name)Guadeloupe 0.025
## factor(ageClass)94.5:factor(reg_name)Guadeloupe NA
## factor(ageClass)14.5:factor(reg_name)Guyane 0.000
## factor(ageClass)24.5:factor(reg_name)Guyane 0.005
## factor(ageClass)34.5:factor(reg_name)Guyane -0.013
## factor(ageClass)44.5:factor(reg_name)Guyane 0.006
## factor(ageClass)54.5:factor(reg_name)Guyane 0.007
## factor(ageClass)64.5:factor(reg_name)Guyane 0.000
## factor(ageClass)74.5:factor(reg_name)Guyane NA
## factor(ageClass)84.5:factor(reg_name)Guyane 0.000
## factor(ageClass)94.5:factor(reg_name)Guyane NA
## factor(ageClass)14.5:factor(reg_name)Hauts-de-France -2.946
## factor(ageClass)24.5:factor(reg_name)Hauts-de-France 1.084
## factor(ageClass)34.5:factor(reg_name)Hauts-de-France 1.555
## factor(ageClass)44.5:factor(reg_name)Hauts-de-France 1.167
## factor(ageClass)54.5:factor(reg_name)Hauts-de-France 2.357
## factor(ageClass)64.5:factor(reg_name)Hauts-de-France 4.582
## factor(ageClass)74.5:factor(reg_name)Hauts-de-France 4.036
## factor(ageClass)84.5:factor(reg_name)Hauts-de-France 4.316
## factor(ageClass)94.5:factor(reg_name)Hauts-de-France 3.378
## factor(ageClass)14.5:factor(reg_name)ÃŽle-de-France -0.332
## factor(ageClass)24.5:factor(reg_name)ÃŽle-de-France -1.430
## factor(ageClass)34.5:factor(reg_name)ÃŽle-de-France 1.319
## factor(ageClass)44.5:factor(reg_name)ÃŽle-de-France 2.269
## factor(ageClass)54.5:factor(reg_name)ÃŽle-de-France 2.426
## factor(ageClass)64.5:factor(reg_name)ÃŽle-de-France 4.594
## factor(ageClass)74.5:factor(reg_name)ÃŽle-de-France 1.333
## factor(ageClass)84.5:factor(reg_name)ÃŽle-de-France -3.448
## factor(ageClass)94.5:factor(reg_name)ÃŽle-de-France -0.674
## factor(ageClass)14.5:factor(reg_name)La Réunion 1.961
## factor(ageClass)24.5:factor(reg_name)La Réunion -2.155
## factor(ageClass)34.5:factor(reg_name)La Réunion 2.831
## factor(ageClass)44.5:factor(reg_name)La Réunion 2.664
## factor(ageClass)54.5:factor(reg_name)La Réunion 2.854
## factor(ageClass)64.5:factor(reg_name)La Réunion 5.990
## factor(ageClass)74.5:factor(reg_name)La Réunion 3.746
## factor(ageClass)84.5:factor(reg_name)La Réunion -0.007
## factor(ageClass)94.5:factor(reg_name)La Réunion -0.002
## factor(ageClass)14.5:factor(reg_name)Martinique 1.528
## factor(ageClass)24.5:factor(reg_name)Martinique 2.490
## factor(ageClass)34.5:factor(reg_name)Martinique 2.189
## factor(ageClass)44.5:factor(reg_name)Martinique 1.202
## factor(ageClass)54.5:factor(reg_name)Martinique 2.285
## factor(ageClass)64.5:factor(reg_name)Martinique 1.778
## factor(ageClass)74.5:factor(reg_name)Martinique 2.580
## factor(ageClass)84.5:factor(reg_name)Martinique -1.190
## factor(ageClass)94.5:factor(reg_name)Martinique 1.521
## factor(ageClass)14.5:factor(reg_name)Mayotte -0.003
## factor(ageClass)24.5:factor(reg_name)Mayotte -0.003
## factor(ageClass)34.5:factor(reg_name)Mayotte -0.003
## factor(ageClass)44.5:factor(reg_name)Mayotte -0.003
## factor(ageClass)54.5:factor(reg_name)Mayotte -0.003
## factor(ageClass)64.5:factor(reg_name)Mayotte -0.002
## factor(ageClass)74.5:factor(reg_name)Mayotte -0.003
## factor(ageClass)84.5:factor(reg_name)Mayotte NA
## factor(ageClass)94.5:factor(reg_name)Mayotte NA
## factor(ageClass)14.5:factor(reg_name)Normandie -0.469
## factor(ageClass)24.5:factor(reg_name)Normandie 1.368
## factor(ageClass)34.5:factor(reg_name)Normandie -2.515
## factor(ageClass)44.5:factor(reg_name)Normandie 2.017
## factor(ageClass)54.5:factor(reg_name)Normandie 1.953
## factor(ageClass)64.5:factor(reg_name)Normandie 3.353
## factor(ageClass)74.5:factor(reg_name)Normandie 0.743
## factor(ageClass)84.5:factor(reg_name)Normandie 0.853
## factor(ageClass)94.5:factor(reg_name)Normandie -0.298
## factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine -2.059
## factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine -2.820
## factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine -4.354
## factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine -1.454
## factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine -4.375
## factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine 0.157
## factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine -4.096
## factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine -3.555
## factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine -5.845
## factor(ageClass)14.5:factor(reg_name)Occitanie -1.596
## factor(ageClass)24.5:factor(reg_name)Occitanie 0.756
## factor(ageClass)34.5:factor(reg_name)Occitanie 1.644
## factor(ageClass)44.5:factor(reg_name)Occitanie 0.682
## factor(ageClass)54.5:factor(reg_name)Occitanie -0.594
## factor(ageClass)64.5:factor(reg_name)Occitanie 1.304
## factor(ageClass)74.5:factor(reg_name)Occitanie 0.988
## factor(ageClass)84.5:factor(reg_name)Occitanie 3.077
## factor(ageClass)94.5:factor(reg_name)Occitanie 4.217
## factor(ageClass)14.5:factor(reg_name)Pays de la Loire -0.027
## factor(ageClass)24.5:factor(reg_name)Pays de la Loire 0.756
## factor(ageClass)34.5:factor(reg_name)Pays de la Loire 1.178
## factor(ageClass)44.5:factor(reg_name)Pays de la Loire 3.332
## factor(ageClass)54.5:factor(reg_name)Pays de la Loire 3.627
## factor(ageClass)64.5:factor(reg_name)Pays de la Loire 4.522
## factor(ageClass)74.5:factor(reg_name)Pays de la Loire 3.901
## factor(ageClass)84.5:factor(reg_name)Pays de la Loire 6.192
## factor(ageClass)94.5:factor(reg_name)Pays de la Loire 5.393
## factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur -3.469
## factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur -2.453
## factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur -1.343
## factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur -2.518
## factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur -0.846
## factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur 1.805
## factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur -5.360
## factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur -2.551
## factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur -2.412
## time:factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté 2.113
## time:factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté -1.486
## time:factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté -0.571
## time:factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté 1.049
## time:factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté 1.263
## time:factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté -0.219
## time:factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté -0.255
## time:factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté -1.226
## time:factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté 1.796
## time:factor(ageClass)14.5:factor(reg_name)Bretagne 2.276
## time:factor(ageClass)24.5:factor(reg_name)Bretagne 5.203
## time:factor(ageClass)34.5:factor(reg_name)Bretagne 1.547
## time:factor(ageClass)44.5:factor(reg_name)Bretagne 0.886
## time:factor(ageClass)54.5:factor(reg_name)Bretagne 1.556
## time:factor(ageClass)64.5:factor(reg_name)Bretagne 1.429
## time:factor(ageClass)74.5:factor(reg_name)Bretagne 0.498
## time:factor(ageClass)84.5:factor(reg_name)Bretagne 3.406
## time:factor(ageClass)94.5:factor(reg_name)Bretagne 3.242
## time:factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire 0.629
## time:factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire -2.174
## time:factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire -2.891
## time:factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire -2.330
## time:factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire -1.770
## time:factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire -3.020
## time:factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire 1.165
## time:factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire -0.852
## time:factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire 1.366
## time:factor(ageClass)14.5:factor(reg_name)Corse 4.399
## time:factor(ageClass)24.5:factor(reg_name)Corse 3.691
## time:factor(ageClass)34.5:factor(reg_name)Corse 4.662
## time:factor(ageClass)44.5:factor(reg_name)Corse 2.259
## time:factor(ageClass)54.5:factor(reg_name)Corse 2.839
## time:factor(ageClass)64.5:factor(reg_name)Corse 4.292
## time:factor(ageClass)74.5:factor(reg_name)Corse 3.829
## time:factor(ageClass)84.5:factor(reg_name)Corse 1.708
## time:factor(ageClass)94.5:factor(reg_name)Corse -1.607
## time:factor(ageClass)14.5:factor(reg_name)Grand Est 5.046
## time:factor(ageClass)24.5:factor(reg_name)Grand Est 1.358
## time:factor(ageClass)34.5:factor(reg_name)Grand Est -0.760
## time:factor(ageClass)44.5:factor(reg_name)Grand Est -0.343
## time:factor(ageClass)54.5:factor(reg_name)Grand Est -1.524
## time:factor(ageClass)64.5:factor(reg_name)Grand Est -1.006
## time:factor(ageClass)74.5:factor(reg_name)Grand Est -0.076
## time:factor(ageClass)84.5:factor(reg_name)Grand Est 2.959
## time:factor(ageClass)94.5:factor(reg_name)Grand Est 1.671
## time:factor(ageClass)14.5:factor(reg_name)Guadeloupe -0.025
## time:factor(ageClass)24.5:factor(reg_name)Guadeloupe -0.025
## time:factor(ageClass)34.5:factor(reg_name)Guadeloupe -0.025
## time:factor(ageClass)44.5:factor(reg_name)Guadeloupe -0.025
## time:factor(ageClass)54.5:factor(reg_name)Guadeloupe -0.025
## time:factor(ageClass)64.5:factor(reg_name)Guadeloupe -0.025
## time:factor(ageClass)74.5:factor(reg_name)Guadeloupe -0.025
## time:factor(ageClass)84.5:factor(reg_name)Guadeloupe -0.022
## time:factor(ageClass)94.5:factor(reg_name)Guadeloupe NA
## time:factor(ageClass)14.5:factor(reg_name)Guyane 0.000
## time:factor(ageClass)24.5:factor(reg_name)Guyane 0.001
## time:factor(ageClass)34.5:factor(reg_name)Guyane 0.030
## time:factor(ageClass)44.5:factor(reg_name)Guyane 0.000
## time:factor(ageClass)54.5:factor(reg_name)Guyane -0.001
## time:factor(ageClass)64.5:factor(reg_name)Guyane 0.000
## time:factor(ageClass)74.5:factor(reg_name)Guyane NA
## time:factor(ageClass)84.5:factor(reg_name)Guyane 0.000
## time:factor(ageClass)94.5:factor(reg_name)Guyane NA
## time:factor(ageClass)14.5:factor(reg_name)Hauts-de-France 5.919
## time:factor(ageClass)24.5:factor(reg_name)Hauts-de-France 1.483
## time:factor(ageClass)34.5:factor(reg_name)Hauts-de-France -0.106
## time:factor(ageClass)44.5:factor(reg_name)Hauts-de-France 0.564
## time:factor(ageClass)54.5:factor(reg_name)Hauts-de-France 0.791
## time:factor(ageClass)64.5:factor(reg_name)Hauts-de-France -1.998
## time:factor(ageClass)74.5:factor(reg_name)Hauts-de-France -2.115
## time:factor(ageClass)84.5:factor(reg_name)Hauts-de-France -0.208
## time:factor(ageClass)94.5:factor(reg_name)Hauts-de-France 2.074
## time:factor(ageClass)14.5:factor(reg_name)ÃŽle-de-France 1.306
## time:factor(ageClass)24.5:factor(reg_name)ÃŽle-de-France 2.102
## time:factor(ageClass)34.5:factor(reg_name)ÃŽle-de-France -0.943
## time:factor(ageClass)44.5:factor(reg_name)ÃŽle-de-France -1.199
## time:factor(ageClass)54.5:factor(reg_name)ÃŽle-de-France -1.236
## time:factor(ageClass)64.5:factor(reg_name)ÃŽle-de-France -2.148
## time:factor(ageClass)74.5:factor(reg_name)ÃŽle-de-France -0.099
## time:factor(ageClass)84.5:factor(reg_name)ÃŽle-de-France 6.036
## time:factor(ageClass)94.5:factor(reg_name)ÃŽle-de-France 3.495
## time:factor(ageClass)14.5:factor(reg_name)La Réunion -1.783
## time:factor(ageClass)24.5:factor(reg_name)La Réunion 1.698
## time:factor(ageClass)34.5:factor(reg_name)La Réunion -2.754
## time:factor(ageClass)44.5:factor(reg_name)La Réunion -2.806
## time:factor(ageClass)54.5:factor(reg_name)La Réunion -2.712
## time:factor(ageClass)64.5:factor(reg_name)La Réunion -4.987
## time:factor(ageClass)74.5:factor(reg_name)La Réunion -3.566
## time:factor(ageClass)84.5:factor(reg_name)La Réunion -0.001
## time:factor(ageClass)94.5:factor(reg_name)La Réunion NA
## time:factor(ageClass)14.5:factor(reg_name)Martinique -1.003
## time:factor(ageClass)24.5:factor(reg_name)Martinique -1.573
## time:factor(ageClass)34.5:factor(reg_name)Martinique -1.825
## time:factor(ageClass)44.5:factor(reg_name)Martinique -0.370
## time:factor(ageClass)54.5:factor(reg_name)Martinique -1.925
## time:factor(ageClass)64.5:factor(reg_name)Martinique -1.578
## time:factor(ageClass)74.5:factor(reg_name)Martinique -2.953
## time:factor(ageClass)84.5:factor(reg_name)Martinique 1.703
## time:factor(ageClass)94.5:factor(reg_name)Martinique -1.121
## time:factor(ageClass)14.5:factor(reg_name)Mayotte 0.000
## time:factor(ageClass)24.5:factor(reg_name)Mayotte 0.000
## time:factor(ageClass)34.5:factor(reg_name)Mayotte 0.000
## time:factor(ageClass)44.5:factor(reg_name)Mayotte 0.000
## time:factor(ageClass)54.5:factor(reg_name)Mayotte 0.000
## time:factor(ageClass)64.5:factor(reg_name)Mayotte 0.000
## time:factor(ageClass)74.5:factor(reg_name)Mayotte 0.000
## time:factor(ageClass)84.5:factor(reg_name)Mayotte NA
## time:factor(ageClass)94.5:factor(reg_name)Mayotte NA
## time:factor(ageClass)14.5:factor(reg_name)Normandie 3.459
## time:factor(ageClass)24.5:factor(reg_name)Normandie 1.524
## time:factor(ageClass)34.5:factor(reg_name)Normandie 4.495
## time:factor(ageClass)44.5:factor(reg_name)Normandie 1.587
## time:factor(ageClass)54.5:factor(reg_name)Normandie 1.102
## time:factor(ageClass)64.5:factor(reg_name)Normandie -2.136
## time:factor(ageClass)74.5:factor(reg_name)Normandie 1.303
## time:factor(ageClass)84.5:factor(reg_name)Normandie 3.834
## time:factor(ageClass)94.5:factor(reg_name)Normandie 3.758
## time:factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine 4.864
## time:factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine 4.248
## time:factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine 3.388
## time:factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine 2.257
## time:factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine 4.417
## time:factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine -0.024
## time:factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine 2.211
## time:factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine 4.227
## time:factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine 3.080
## time:factor(ageClass)14.5:factor(reg_name)Occitanie 1.148
## time:factor(ageClass)24.5:factor(reg_name)Occitanie -1.357
## time:factor(ageClass)34.5:factor(reg_name)Occitanie -1.397
## time:factor(ageClass)44.5:factor(reg_name)Occitanie -1.336
## time:factor(ageClass)54.5:factor(reg_name)Occitanie 0.133
## time:factor(ageClass)64.5:factor(reg_name)Occitanie -2.461
## time:factor(ageClass)74.5:factor(reg_name)Occitanie -2.186
## time:factor(ageClass)84.5:factor(reg_name)Occitanie -1.029
## time:factor(ageClass)94.5:factor(reg_name)Occitanie -3.333
## time:factor(ageClass)14.5:factor(reg_name)Pays de la Loire 1.263
## time:factor(ageClass)24.5:factor(reg_name)Pays de la Loire 1.200
## time:factor(ageClass)34.5:factor(reg_name)Pays de la Loire 0.034
## time:factor(ageClass)44.5:factor(reg_name)Pays de la Loire -1.882
## time:factor(ageClass)54.5:factor(reg_name)Pays de la Loire -1.391
## time:factor(ageClass)64.5:factor(reg_name)Pays de la Loire -3.204
## time:factor(ageClass)74.5:factor(reg_name)Pays de la Loire -1.772
## time:factor(ageClass)84.5:factor(reg_name)Pays de la Loire -2.491
## time:factor(ageClass)94.5:factor(reg_name)Pays de la Loire -3.586
## time:factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur 3.761
## time:factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur 1.255
## time:factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.058
## time:factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur 1.483
## time:factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur 1.256
## time:factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur -0.714
## time:factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur 2.825
## time:factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur 4.729
## time:factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur 3.567
## Pr(>|z|)
## (Intercept) 5.77e-05
## time < 2e-16
## factor(ageClass)14.5 0.914274
## factor(ageClass)24.5 3.11e-05
## factor(ageClass)34.5 0.000235
## factor(ageClass)44.5 1.50e-05
## factor(ageClass)54.5 1.17e-11
## factor(ageClass)64.5 < 2e-16
## factor(ageClass)74.5 < 2e-16
## factor(ageClass)84.5 < 2e-16
## factor(ageClass)94.5 < 2e-16
## factor(reg_name)Bourgogne-Franche-Comté 3.27e-08
## factor(reg_name)Bretagne 2.89e-13
## factor(reg_name)Centre-Val de Loire 0.821624
## factor(reg_name)Corse 1.01e-08
## factor(reg_name)Grand Est < 2e-16
## factor(reg_name)Guadeloupe 0.980137
## factor(reg_name)Guyane 0.995588
## factor(reg_name)Hauts-de-France < 2e-16
## factor(reg_name)ÃŽle-de-France < 2e-16
## factor(reg_name)La Réunion 2.86e-12
## factor(reg_name)Martinique 0.087289
## factor(reg_name)Mayotte 0.998850
## factor(reg_name)Normandie 0.175614
## factor(reg_name)Nouvelle-Aquitaine 0.006593
## factor(reg_name)Occitanie 0.000221
## factor(reg_name)Pays de la Loire 0.005717
## factor(reg_name)Provence-Alpes-Côte d'Azur 2.97e-13
## time:factor(ageClass)14.5 0.006293
## time:factor(ageClass)24.5 0.586954
## time:factor(ageClass)34.5 0.119980
## time:factor(ageClass)44.5 0.116589
## time:factor(ageClass)54.5 0.065265
## time:factor(ageClass)64.5 3.96e-05
## time:factor(ageClass)74.5 5.29e-05
## time:factor(ageClass)84.5 0.516734
## time:factor(ageClass)94.5 0.795146
## time:factor(reg_name)Bourgogne-Franche-Comté 0.524547
## time:factor(reg_name)Bretagne 0.010011
## time:factor(reg_name)Centre-Val de Loire 0.108699
## time:factor(reg_name)Corse 1.93e-05
## time:factor(reg_name)Grand Est 0.769810
## time:factor(reg_name)Guadeloupe 0.980101
## time:factor(reg_name)Guyane 0.999865
## time:factor(reg_name)Hauts-de-France 0.003723
## time:factor(reg_name)ÃŽle-de-France 3.13e-05
## time:factor(reg_name)La Réunion 0.482642
## time:factor(reg_name)Martinique 0.123346
## time:factor(reg_name)Mayotte 0.999968
## time:factor(reg_name)Normandie 0.973897
## time:factor(reg_name)Nouvelle-Aquitaine 0.002855
## time:factor(reg_name)Occitanie 0.330854
## time:factor(reg_name)Pays de la Loire 0.750614
## time:factor(reg_name)Provence-Alpes-Côte d'Azur 0.544372
## factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté 0.104442
## factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté 0.067190
## factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté 0.707270
## factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté 0.407488
## factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté 0.294796
## factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté 0.322664
## factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté 0.204442
## factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté 0.062764
## factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté 0.648069
## factor(ageClass)14.5:factor(reg_name)Bretagne 0.058952
## factor(ageClass)24.5:factor(reg_name)Bretagne 0.007334
## factor(ageClass)34.5:factor(reg_name)Bretagne 0.051874
## factor(ageClass)44.5:factor(reg_name)Bretagne 0.674267
## factor(ageClass)54.5:factor(reg_name)Bretagne 0.694927
## factor(ageClass)64.5:factor(reg_name)Bretagne 0.321245
## factor(ageClass)74.5:factor(reg_name)Bretagne 0.267640
## factor(ageClass)84.5:factor(reg_name)Bretagne 0.621036
## factor(ageClass)94.5:factor(reg_name)Bretagne 0.383911
## factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire 0.976097
## factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire 0.546474
## factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire 0.129420
## factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire 0.092869
## factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire 0.200906
## factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire 0.017771
## factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire 0.366495
## factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire 0.129785
## factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire 0.795474
## factor(ageClass)14.5:factor(reg_name)Corse 2.23e-06
## factor(ageClass)24.5:factor(reg_name)Corse 0.000241
## factor(ageClass)34.5:factor(reg_name)Corse 1.23e-05
## factor(ageClass)44.5:factor(reg_name)Corse 0.005707
## factor(ageClass)54.5:factor(reg_name)Corse 0.010818
## factor(ageClass)64.5:factor(reg_name)Corse 0.001613
## factor(ageClass)74.5:factor(reg_name)Corse 0.002822
## factor(ageClass)84.5:factor(reg_name)Corse 0.309220
## factor(ageClass)94.5:factor(reg_name)Corse 0.048140
## factor(ageClass)14.5:factor(reg_name)Grand Est 0.000261
## factor(ageClass)24.5:factor(reg_name)Grand Est 0.009603
## factor(ageClass)34.5:factor(reg_name)Grand Est 0.012898
## factor(ageClass)44.5:factor(reg_name)Grand Est 0.007367
## factor(ageClass)54.5:factor(reg_name)Grand Est 0.000181
## factor(ageClass)64.5:factor(reg_name)Grand Est 1.87e-07
## factor(ageClass)74.5:factor(reg_name)Grand Est 0.046682
## factor(ageClass)84.5:factor(reg_name)Grand Est 0.032226
## factor(ageClass)94.5:factor(reg_name)Grand Est 0.009094
## factor(ageClass)14.5:factor(reg_name)Guadeloupe 0.980055
## factor(ageClass)24.5:factor(reg_name)Guadeloupe 0.979962
## factor(ageClass)34.5:factor(reg_name)Guadeloupe 0.980142
## factor(ageClass)44.5:factor(reg_name)Guadeloupe 0.979917
## factor(ageClass)54.5:factor(reg_name)Guadeloupe 0.979981
## factor(ageClass)64.5:factor(reg_name)Guadeloupe 0.980116
## factor(ageClass)74.5:factor(reg_name)Guadeloupe 0.979715
## factor(ageClass)84.5:factor(reg_name)Guadeloupe 0.979728
## factor(ageClass)94.5:factor(reg_name)Guadeloupe NA
## factor(ageClass)14.5:factor(reg_name)Guyane 0.999824
## factor(ageClass)24.5:factor(reg_name)Guyane 0.995917
## factor(ageClass)34.5:factor(reg_name)Guyane 0.989317
## factor(ageClass)44.5:factor(reg_name)Guyane 0.995430
## factor(ageClass)54.5:factor(reg_name)Guyane 0.994075
## factor(ageClass)64.5:factor(reg_name)Guyane 0.999943
## factor(ageClass)74.5:factor(reg_name)Guyane NA
## factor(ageClass)84.5:factor(reg_name)Guyane 0.999866
## factor(ageClass)94.5:factor(reg_name)Guyane NA
## factor(ageClass)14.5:factor(reg_name)Hauts-de-France 0.003215
## factor(ageClass)24.5:factor(reg_name)Hauts-de-France 0.278257
## factor(ageClass)34.5:factor(reg_name)Hauts-de-France 0.119951
## factor(ageClass)44.5:factor(reg_name)Hauts-de-France 0.243209
## factor(ageClass)54.5:factor(reg_name)Hauts-de-France 0.018404
## factor(ageClass)64.5:factor(reg_name)Hauts-de-France 4.62e-06
## factor(ageClass)74.5:factor(reg_name)Hauts-de-France 5.43e-05
## factor(ageClass)84.5:factor(reg_name)Hauts-de-France 1.59e-05
## factor(ageClass)94.5:factor(reg_name)Hauts-de-France 0.000730
## factor(ageClass)14.5:factor(reg_name)ÃŽle-de-France 0.739777
## factor(ageClass)24.5:factor(reg_name)ÃŽle-de-France 0.152624
## factor(ageClass)34.5:factor(reg_name)ÃŽle-de-France 0.187128
## factor(ageClass)44.5:factor(reg_name)ÃŽle-de-France 0.023245
## factor(ageClass)54.5:factor(reg_name)ÃŽle-de-France 0.015278
## factor(ageClass)64.5:factor(reg_name)ÃŽle-de-France 4.35e-06
## factor(ageClass)74.5:factor(reg_name)ÃŽle-de-France 0.182613
## factor(ageClass)84.5:factor(reg_name)ÃŽle-de-France 0.000565
## factor(ageClass)94.5:factor(reg_name)ÃŽle-de-France 0.500388
## factor(ageClass)14.5:factor(reg_name)La Réunion 0.049861
## factor(ageClass)24.5:factor(reg_name)La Réunion 0.031129
## factor(ageClass)34.5:factor(reg_name)La Réunion 0.004645
## factor(ageClass)44.5:factor(reg_name)La Réunion 0.007711
## factor(ageClass)54.5:factor(reg_name)La Réunion 0.004322
## factor(ageClass)64.5:factor(reg_name)La Réunion 2.10e-09
## factor(ageClass)74.5:factor(reg_name)La Réunion 0.000179
## factor(ageClass)84.5:factor(reg_name)La Réunion 0.994644
## factor(ageClass)94.5:factor(reg_name)La Réunion 0.998122
## factor(ageClass)14.5:factor(reg_name)Martinique 0.126434
## factor(ageClass)24.5:factor(reg_name)Martinique 0.012768
## factor(ageClass)34.5:factor(reg_name)Martinique 0.028591
## factor(ageClass)44.5:factor(reg_name)Martinique 0.229297
## factor(ageClass)54.5:factor(reg_name)Martinique 0.022340
## factor(ageClass)64.5:factor(reg_name)Martinique 0.075373
## factor(ageClass)74.5:factor(reg_name)Martinique 0.009873
## factor(ageClass)84.5:factor(reg_name)Martinique 0.233965
## factor(ageClass)94.5:factor(reg_name)Martinique 0.128267
## factor(ageClass)14.5:factor(reg_name)Mayotte 0.997754
## factor(ageClass)24.5:factor(reg_name)Mayotte 0.997700
## factor(ageClass)34.5:factor(reg_name)Mayotte 0.997719
## factor(ageClass)44.5:factor(reg_name)Mayotte 0.997710
## factor(ageClass)54.5:factor(reg_name)Mayotte 0.997704
## factor(ageClass)64.5:factor(reg_name)Mayotte 0.998565
## factor(ageClass)74.5:factor(reg_name)Mayotte 0.997818
## factor(ageClass)84.5:factor(reg_name)Mayotte NA
## factor(ageClass)94.5:factor(reg_name)Mayotte NA
## factor(ageClass)14.5:factor(reg_name)Normandie 0.639266
## factor(ageClass)24.5:factor(reg_name)Normandie 0.171262
## factor(ageClass)34.5:factor(reg_name)Normandie 0.011895
## factor(ageClass)44.5:factor(reg_name)Normandie 0.043725
## factor(ageClass)54.5:factor(reg_name)Normandie 0.050841
## factor(ageClass)64.5:factor(reg_name)Normandie 0.000799
## factor(ageClass)74.5:factor(reg_name)Normandie 0.457475
## factor(ageClass)84.5:factor(reg_name)Normandie 0.393435
## factor(ageClass)94.5:factor(reg_name)Normandie 0.765608
## factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine 0.039518
## factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine 0.004810
## factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine 1.34e-05
## factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine 0.146026
## factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine 1.22e-05
## factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine 0.875290
## factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine 4.21e-05
## factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine 0.000377
## factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine 5.07e-09
## factor(ageClass)14.5:factor(reg_name)Occitanie 0.110488
## factor(ageClass)24.5:factor(reg_name)Occitanie 0.449529
## factor(ageClass)34.5:factor(reg_name)Occitanie 0.100267
## factor(ageClass)44.5:factor(reg_name)Occitanie 0.495442
## factor(ageClass)54.5:factor(reg_name)Occitanie 0.552621
## factor(ageClass)64.5:factor(reg_name)Occitanie 0.192232
## factor(ageClass)74.5:factor(reg_name)Occitanie 0.323188
## factor(ageClass)84.5:factor(reg_name)Occitanie 0.002089
## factor(ageClass)94.5:factor(reg_name)Occitanie 2.47e-05
## factor(ageClass)14.5:factor(reg_name)Pays de la Loire 0.978700
## factor(ageClass)24.5:factor(reg_name)Pays de la Loire 0.449411
## factor(ageClass)34.5:factor(reg_name)Pays de la Loire 0.238756
## factor(ageClass)44.5:factor(reg_name)Pays de la Loire 0.000863
## factor(ageClass)54.5:factor(reg_name)Pays de la Loire 0.000287
## factor(ageClass)64.5:factor(reg_name)Pays de la Loire 6.12e-06
## factor(ageClass)74.5:factor(reg_name)Pays de la Loire 9.56e-05
## factor(ageClass)84.5:factor(reg_name)Pays de la Loire 5.93e-10
## factor(ageClass)94.5:factor(reg_name)Pays de la Loire 6.91e-08
## factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.000522
## factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.014167
## factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.179320
## factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.011786
## factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.397408
## factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.071111
## factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur 8.33e-08
## factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.010754
## factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.015861
## time:factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté 0.034639
## time:factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté 0.137256
## time:factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté 0.568178
## time:factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté 0.294276
## time:factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté 0.206623
## time:factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté 0.826264
## time:factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté 0.798678
## time:factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté 0.220199
## time:factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté 0.072536
## time:factor(ageClass)14.5:factor(reg_name)Bretagne 0.022863
## time:factor(ageClass)24.5:factor(reg_name)Bretagne 1.96e-07
## time:factor(ageClass)34.5:factor(reg_name)Bretagne 0.121918
## time:factor(ageClass)44.5:factor(reg_name)Bretagne 0.375443
## time:factor(ageClass)54.5:factor(reg_name)Bretagne 0.119680
## time:factor(ageClass)64.5:factor(reg_name)Bretagne 0.152885
## time:factor(ageClass)74.5:factor(reg_name)Bretagne 0.618749
## time:factor(ageClass)84.5:factor(reg_name)Bretagne 0.000659
## time:factor(ageClass)94.5:factor(reg_name)Bretagne 0.001188
## time:factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire 0.529128
## time:factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire 0.029737
## time:factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire 0.003846
## time:factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire 0.019818
## time:factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire 0.076800
## time:factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire 0.002531
## time:factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire 0.243975
## time:factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire 0.394145
## time:factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire 0.172009
## time:factor(ageClass)14.5:factor(reg_name)Corse 1.09e-05
## time:factor(ageClass)24.5:factor(reg_name)Corse 0.000223
## time:factor(ageClass)34.5:factor(reg_name)Corse 3.14e-06
## time:factor(ageClass)44.5:factor(reg_name)Corse 0.023887
## time:factor(ageClass)54.5:factor(reg_name)Corse 0.004523
## time:factor(ageClass)64.5:factor(reg_name)Corse 1.77e-05
## time:factor(ageClass)74.5:factor(reg_name)Corse 0.000129
## time:factor(ageClass)84.5:factor(reg_name)Corse 0.087697
## time:factor(ageClass)94.5:factor(reg_name)Corse 0.108159
## time:factor(ageClass)14.5:factor(reg_name)Grand Est 4.52e-07
## time:factor(ageClass)24.5:factor(reg_name)Grand Est 0.174550
## time:factor(ageClass)34.5:factor(reg_name)Grand Est 0.447357
## time:factor(ageClass)44.5:factor(reg_name)Grand Est 0.731724
## time:factor(ageClass)54.5:factor(reg_name)Grand Est 0.127468
## time:factor(ageClass)64.5:factor(reg_name)Grand Est 0.314515
## time:factor(ageClass)74.5:factor(reg_name)Grand Est 0.939533
## time:factor(ageClass)84.5:factor(reg_name)Grand Est 0.003083
## time:factor(ageClass)94.5:factor(reg_name)Grand Est 0.094753
## time:factor(ageClass)14.5:factor(reg_name)Guadeloupe 0.980258
## time:factor(ageClass)24.5:factor(reg_name)Guadeloupe 0.980252
## time:factor(ageClass)34.5:factor(reg_name)Guadeloupe 0.980353
## time:factor(ageClass)44.5:factor(reg_name)Guadeloupe 0.980064
## time:factor(ageClass)54.5:factor(reg_name)Guadeloupe 0.980090
## time:factor(ageClass)64.5:factor(reg_name)Guadeloupe 0.980297
## time:factor(ageClass)74.5:factor(reg_name)Guadeloupe 0.979789
## time:factor(ageClass)84.5:factor(reg_name)Guadeloupe 0.982112
## time:factor(ageClass)94.5:factor(reg_name)Guadeloupe NA
## time:factor(ageClass)14.5:factor(reg_name)Guyane 0.999898
## time:factor(ageClass)24.5:factor(reg_name)Guyane 0.999552
## time:factor(ageClass)34.5:factor(reg_name)Guyane 0.976207
## time:factor(ageClass)44.5:factor(reg_name)Guyane 0.999721
## time:factor(ageClass)54.5:factor(reg_name)Guyane 0.998976
## time:factor(ageClass)64.5:factor(reg_name)Guyane 0.999985
## time:factor(ageClass)74.5:factor(reg_name)Guyane NA
## time:factor(ageClass)84.5:factor(reg_name)Guyane 0.999998
## time:factor(ageClass)94.5:factor(reg_name)Guyane NA
## time:factor(ageClass)14.5:factor(reg_name)Hauts-de-France 3.24e-09
## time:factor(ageClass)24.5:factor(reg_name)Hauts-de-France 0.138138
## time:factor(ageClass)34.5:factor(reg_name)Hauts-de-France 0.915620
## time:factor(ageClass)44.5:factor(reg_name)Hauts-de-France 0.572848
## time:factor(ageClass)54.5:factor(reg_name)Hauts-de-France 0.429055
## time:factor(ageClass)64.5:factor(reg_name)Hauts-de-France 0.045694
## time:factor(ageClass)74.5:factor(reg_name)Hauts-de-France 0.034445
## time:factor(ageClass)84.5:factor(reg_name)Hauts-de-France 0.834904
## time:factor(ageClass)94.5:factor(reg_name)Hauts-de-France 0.038036
## time:factor(ageClass)14.5:factor(reg_name)ÃŽle-de-France 0.191452
## time:factor(ageClass)24.5:factor(reg_name)ÃŽle-de-France 0.035519
## time:factor(ageClass)34.5:factor(reg_name)ÃŽle-de-France 0.345912
## time:factor(ageClass)44.5:factor(reg_name)ÃŽle-de-France 0.230374
## time:factor(ageClass)54.5:factor(reg_name)ÃŽle-de-France 0.216395
## time:factor(ageClass)64.5:factor(reg_name)ÃŽle-de-France 0.031747
## time:factor(ageClass)74.5:factor(reg_name)ÃŽle-de-France 0.920835
## time:factor(ageClass)84.5:factor(reg_name)ÃŽle-de-France 1.58e-09
## time:factor(ageClass)94.5:factor(reg_name)ÃŽle-de-France 0.000474
## time:factor(ageClass)14.5:factor(reg_name)La Réunion 0.074557
## time:factor(ageClass)24.5:factor(reg_name)La Réunion 0.089454
## time:factor(ageClass)34.5:factor(reg_name)La Réunion 0.005890
## time:factor(ageClass)44.5:factor(reg_name)La Réunion 0.005010
## time:factor(ageClass)54.5:factor(reg_name)La Réunion 0.006686
## time:factor(ageClass)64.5:factor(reg_name)La Réunion 6.14e-07
## time:factor(ageClass)74.5:factor(reg_name)La Réunion 0.000363
## time:factor(ageClass)84.5:factor(reg_name)La Réunion 0.999485
## time:factor(ageClass)94.5:factor(reg_name)La Réunion NA
## time:factor(ageClass)14.5:factor(reg_name)Martinique 0.315998
## time:factor(ageClass)24.5:factor(reg_name)Martinique 0.115686
## time:factor(ageClass)34.5:factor(reg_name)Martinique 0.068050
## time:factor(ageClass)44.5:factor(reg_name)Martinique 0.711263
## time:factor(ageClass)54.5:factor(reg_name)Martinique 0.054168
## time:factor(ageClass)64.5:factor(reg_name)Martinique 0.114524
## time:factor(ageClass)74.5:factor(reg_name)Martinique 0.003144
## time:factor(ageClass)84.5:factor(reg_name)Martinique 0.088548
## time:factor(ageClass)94.5:factor(reg_name)Martinique 0.262260
## time:factor(ageClass)14.5:factor(reg_name)Mayotte 0.999927
## time:factor(ageClass)24.5:factor(reg_name)Mayotte 0.999918
## time:factor(ageClass)34.5:factor(reg_name)Mayotte 0.999960
## time:factor(ageClass)44.5:factor(reg_name)Mayotte 0.999944
## time:factor(ageClass)54.5:factor(reg_name)Mayotte 0.999918
## time:factor(ageClass)64.5:factor(reg_name)Mayotte 0.999986
## time:factor(ageClass)74.5:factor(reg_name)Mayotte 0.999970
## time:factor(ageClass)84.5:factor(reg_name)Mayotte NA
## time:factor(ageClass)94.5:factor(reg_name)Mayotte NA
## time:factor(ageClass)14.5:factor(reg_name)Normandie 0.000543
## time:factor(ageClass)24.5:factor(reg_name)Normandie 0.127555
## time:factor(ageClass)34.5:factor(reg_name)Normandie 6.96e-06
## time:factor(ageClass)44.5:factor(reg_name)Normandie 0.112447
## time:factor(ageClass)54.5:factor(reg_name)Normandie 0.270554
## time:factor(ageClass)64.5:factor(reg_name)Normandie 0.032705
## time:factor(ageClass)74.5:factor(reg_name)Normandie 0.192578
## time:factor(ageClass)84.5:factor(reg_name)Normandie 0.000126
## time:factor(ageClass)94.5:factor(reg_name)Normandie 0.000171
## time:factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine 1.15e-06
## time:factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine 2.16e-05
## time:factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine 0.000705
## time:factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine 0.024018
## time:factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine 1.00e-05
## time:factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine 0.980549
## time:factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine 0.027052
## time:factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine 2.37e-05
## time:factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine 0.002071
## time:factor(ageClass)14.5:factor(reg_name)Occitanie 0.250787
## time:factor(ageClass)24.5:factor(reg_name)Occitanie 0.174923
## time:factor(ageClass)34.5:factor(reg_name)Occitanie 0.162450
## time:factor(ageClass)44.5:factor(reg_name)Occitanie 0.181427
## time:factor(ageClass)54.5:factor(reg_name)Occitanie 0.893862
## time:factor(ageClass)64.5:factor(reg_name)Occitanie 0.013858
## time:factor(ageClass)74.5:factor(reg_name)Occitanie 0.028781
## time:factor(ageClass)84.5:factor(reg_name)Occitanie 0.303292
## time:factor(ageClass)94.5:factor(reg_name)Occitanie 0.000860
## time:factor(ageClass)14.5:factor(reg_name)Pays de la Loire 0.206675
## time:factor(ageClass)24.5:factor(reg_name)Pays de la Loire 0.230262
## time:factor(ageClass)34.5:factor(reg_name)Pays de la Loire 0.973139
## time:factor(ageClass)44.5:factor(reg_name)Pays de la Loire 0.059835
## time:factor(ageClass)54.5:factor(reg_name)Pays de la Loire 0.164168
## time:factor(ageClass)64.5:factor(reg_name)Pays de la Loire 0.001355
## time:factor(ageClass)74.5:factor(reg_name)Pays de la Loire 0.076351
## time:factor(ageClass)84.5:factor(reg_name)Pays de la Loire 0.012728
## time:factor(ageClass)94.5:factor(reg_name)Pays de la Loire 0.000336
## time:factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.000170
## time:factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.209481
## time:factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.954076
## time:factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.138076
## time:factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.209210
## time:factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.475071
## time:factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.004734
## time:factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur 2.25e-06
## time:factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.000361
##
## (Intercept) ***
## time ***
## factor(ageClass)14.5
## factor(ageClass)24.5 ***
## factor(ageClass)34.5 ***
## factor(ageClass)44.5 ***
## factor(ageClass)54.5 ***
## factor(ageClass)64.5 ***
## factor(ageClass)74.5 ***
## factor(ageClass)84.5 ***
## factor(ageClass)94.5 ***
## factor(reg_name)Bourgogne-Franche-Comté ***
## factor(reg_name)Bretagne ***
## factor(reg_name)Centre-Val de Loire
## factor(reg_name)Corse ***
## factor(reg_name)Grand Est ***
## factor(reg_name)Guadeloupe
## factor(reg_name)Guyane
## factor(reg_name)Hauts-de-France ***
## factor(reg_name)ÃŽle-de-France ***
## factor(reg_name)La Réunion ***
## factor(reg_name)Martinique .
## factor(reg_name)Mayotte
## factor(reg_name)Normandie
## factor(reg_name)Nouvelle-Aquitaine **
## factor(reg_name)Occitanie ***
## factor(reg_name)Pays de la Loire **
## factor(reg_name)Provence-Alpes-Côte d'Azur ***
## time:factor(ageClass)14.5 **
## time:factor(ageClass)24.5
## time:factor(ageClass)34.5
## time:factor(ageClass)44.5
## time:factor(ageClass)54.5 .
## time:factor(ageClass)64.5 ***
## time:factor(ageClass)74.5 ***
## time:factor(ageClass)84.5
## time:factor(ageClass)94.5
## time:factor(reg_name)Bourgogne-Franche-Comté
## time:factor(reg_name)Bretagne *
## time:factor(reg_name)Centre-Val de Loire
## time:factor(reg_name)Corse ***
## time:factor(reg_name)Grand Est
## time:factor(reg_name)Guadeloupe
## time:factor(reg_name)Guyane
## time:factor(reg_name)Hauts-de-France **
## time:factor(reg_name)ÃŽle-de-France ***
## time:factor(reg_name)La Réunion
## time:factor(reg_name)Martinique
## time:factor(reg_name)Mayotte
## time:factor(reg_name)Normandie
## time:factor(reg_name)Nouvelle-Aquitaine **
## time:factor(reg_name)Occitanie
## time:factor(reg_name)Pays de la Loire
## time:factor(reg_name)Provence-Alpes-Côte d'Azur
## factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté
## factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté .
## factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté
## factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté
## factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté
## factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté
## factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté
## factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté .
## factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté
## factor(ageClass)14.5:factor(reg_name)Bretagne .
## factor(ageClass)24.5:factor(reg_name)Bretagne **
## factor(ageClass)34.5:factor(reg_name)Bretagne .
## factor(ageClass)44.5:factor(reg_name)Bretagne
## factor(ageClass)54.5:factor(reg_name)Bretagne
## factor(ageClass)64.5:factor(reg_name)Bretagne
## factor(ageClass)74.5:factor(reg_name)Bretagne
## factor(ageClass)84.5:factor(reg_name)Bretagne
## factor(ageClass)94.5:factor(reg_name)Bretagne
## factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire
## factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire
## factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire
## factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire .
## factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire
## factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire *
## factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire
## factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire
## factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire
## factor(ageClass)14.5:factor(reg_name)Corse ***
## factor(ageClass)24.5:factor(reg_name)Corse ***
## factor(ageClass)34.5:factor(reg_name)Corse ***
## factor(ageClass)44.5:factor(reg_name)Corse **
## factor(ageClass)54.5:factor(reg_name)Corse *
## factor(ageClass)64.5:factor(reg_name)Corse **
## factor(ageClass)74.5:factor(reg_name)Corse **
## factor(ageClass)84.5:factor(reg_name)Corse
## factor(ageClass)94.5:factor(reg_name)Corse *
## factor(ageClass)14.5:factor(reg_name)Grand Est ***
## factor(ageClass)24.5:factor(reg_name)Grand Est **
## factor(ageClass)34.5:factor(reg_name)Grand Est *
## factor(ageClass)44.5:factor(reg_name)Grand Est **
## factor(ageClass)54.5:factor(reg_name)Grand Est ***
## factor(ageClass)64.5:factor(reg_name)Grand Est ***
## factor(ageClass)74.5:factor(reg_name)Grand Est *
## factor(ageClass)84.5:factor(reg_name)Grand Est *
## factor(ageClass)94.5:factor(reg_name)Grand Est **
## factor(ageClass)14.5:factor(reg_name)Guadeloupe
## factor(ageClass)24.5:factor(reg_name)Guadeloupe
## factor(ageClass)34.5:factor(reg_name)Guadeloupe
## factor(ageClass)44.5:factor(reg_name)Guadeloupe
## factor(ageClass)54.5:factor(reg_name)Guadeloupe
## factor(ageClass)64.5:factor(reg_name)Guadeloupe
## factor(ageClass)74.5:factor(reg_name)Guadeloupe
## factor(ageClass)84.5:factor(reg_name)Guadeloupe
## factor(ageClass)94.5:factor(reg_name)Guadeloupe
## factor(ageClass)14.5:factor(reg_name)Guyane
## factor(ageClass)24.5:factor(reg_name)Guyane
## factor(ageClass)34.5:factor(reg_name)Guyane
## factor(ageClass)44.5:factor(reg_name)Guyane
## factor(ageClass)54.5:factor(reg_name)Guyane
## factor(ageClass)64.5:factor(reg_name)Guyane
## factor(ageClass)74.5:factor(reg_name)Guyane
## factor(ageClass)84.5:factor(reg_name)Guyane
## factor(ageClass)94.5:factor(reg_name)Guyane
## factor(ageClass)14.5:factor(reg_name)Hauts-de-France **
## factor(ageClass)24.5:factor(reg_name)Hauts-de-France
## factor(ageClass)34.5:factor(reg_name)Hauts-de-France
## factor(ageClass)44.5:factor(reg_name)Hauts-de-France
## factor(ageClass)54.5:factor(reg_name)Hauts-de-France *
## factor(ageClass)64.5:factor(reg_name)Hauts-de-France ***
## factor(ageClass)74.5:factor(reg_name)Hauts-de-France ***
## factor(ageClass)84.5:factor(reg_name)Hauts-de-France ***
## factor(ageClass)94.5:factor(reg_name)Hauts-de-France ***
## factor(ageClass)14.5:factor(reg_name)ÃŽle-de-France
## factor(ageClass)24.5:factor(reg_name)ÃŽle-de-France
## factor(ageClass)34.5:factor(reg_name)ÃŽle-de-France
## factor(ageClass)44.5:factor(reg_name)ÃŽle-de-France *
## factor(ageClass)54.5:factor(reg_name)ÃŽle-de-France *
## factor(ageClass)64.5:factor(reg_name)ÃŽle-de-France ***
## factor(ageClass)74.5:factor(reg_name)ÃŽle-de-France
## factor(ageClass)84.5:factor(reg_name)ÃŽle-de-France ***
## factor(ageClass)94.5:factor(reg_name)ÃŽle-de-France
## factor(ageClass)14.5:factor(reg_name)La Réunion *
## factor(ageClass)24.5:factor(reg_name)La Réunion *
## factor(ageClass)34.5:factor(reg_name)La Réunion **
## factor(ageClass)44.5:factor(reg_name)La Réunion **
## factor(ageClass)54.5:factor(reg_name)La Réunion **
## factor(ageClass)64.5:factor(reg_name)La Réunion ***
## factor(ageClass)74.5:factor(reg_name)La Réunion ***
## factor(ageClass)84.5:factor(reg_name)La Réunion
## factor(ageClass)94.5:factor(reg_name)La Réunion
## factor(ageClass)14.5:factor(reg_name)Martinique
## factor(ageClass)24.5:factor(reg_name)Martinique *
## factor(ageClass)34.5:factor(reg_name)Martinique *
## factor(ageClass)44.5:factor(reg_name)Martinique
## factor(ageClass)54.5:factor(reg_name)Martinique *
## factor(ageClass)64.5:factor(reg_name)Martinique .
## factor(ageClass)74.5:factor(reg_name)Martinique **
## factor(ageClass)84.5:factor(reg_name)Martinique
## factor(ageClass)94.5:factor(reg_name)Martinique
## factor(ageClass)14.5:factor(reg_name)Mayotte
## factor(ageClass)24.5:factor(reg_name)Mayotte
## factor(ageClass)34.5:factor(reg_name)Mayotte
## factor(ageClass)44.5:factor(reg_name)Mayotte
## factor(ageClass)54.5:factor(reg_name)Mayotte
## factor(ageClass)64.5:factor(reg_name)Mayotte
## factor(ageClass)74.5:factor(reg_name)Mayotte
## factor(ageClass)84.5:factor(reg_name)Mayotte
## factor(ageClass)94.5:factor(reg_name)Mayotte
## factor(ageClass)14.5:factor(reg_name)Normandie
## factor(ageClass)24.5:factor(reg_name)Normandie
## factor(ageClass)34.5:factor(reg_name)Normandie *
## factor(ageClass)44.5:factor(reg_name)Normandie *
## factor(ageClass)54.5:factor(reg_name)Normandie .
## factor(ageClass)64.5:factor(reg_name)Normandie ***
## factor(ageClass)74.5:factor(reg_name)Normandie
## factor(ageClass)84.5:factor(reg_name)Normandie
## factor(ageClass)94.5:factor(reg_name)Normandie
## factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine *
## factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine **
## factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine ***
## factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine
## factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine ***
## factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine
## factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine ***
## factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine ***
## factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine ***
## factor(ageClass)14.5:factor(reg_name)Occitanie
## factor(ageClass)24.5:factor(reg_name)Occitanie
## factor(ageClass)34.5:factor(reg_name)Occitanie
## factor(ageClass)44.5:factor(reg_name)Occitanie
## factor(ageClass)54.5:factor(reg_name)Occitanie
## factor(ageClass)64.5:factor(reg_name)Occitanie
## factor(ageClass)74.5:factor(reg_name)Occitanie
## factor(ageClass)84.5:factor(reg_name)Occitanie **
## factor(ageClass)94.5:factor(reg_name)Occitanie ***
## factor(ageClass)14.5:factor(reg_name)Pays de la Loire
## factor(ageClass)24.5:factor(reg_name)Pays de la Loire
## factor(ageClass)34.5:factor(reg_name)Pays de la Loire
## factor(ageClass)44.5:factor(reg_name)Pays de la Loire ***
## factor(ageClass)54.5:factor(reg_name)Pays de la Loire ***
## factor(ageClass)64.5:factor(reg_name)Pays de la Loire ***
## factor(ageClass)74.5:factor(reg_name)Pays de la Loire ***
## factor(ageClass)84.5:factor(reg_name)Pays de la Loire ***
## factor(ageClass)94.5:factor(reg_name)Pays de la Loire ***
## factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur ***
## factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur *
## factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur
## factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur *
## factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur
## factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur .
## factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur ***
## factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur *
## factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur *
## time:factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté *
## time:factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté
## time:factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté
## time:factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté
## time:factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté
## time:factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté
## time:factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté
## time:factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté
## time:factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté .
## time:factor(ageClass)14.5:factor(reg_name)Bretagne *
## time:factor(ageClass)24.5:factor(reg_name)Bretagne ***
## time:factor(ageClass)34.5:factor(reg_name)Bretagne
## time:factor(ageClass)44.5:factor(reg_name)Bretagne
## time:factor(ageClass)54.5:factor(reg_name)Bretagne
## time:factor(ageClass)64.5:factor(reg_name)Bretagne
## time:factor(ageClass)74.5:factor(reg_name)Bretagne
## time:factor(ageClass)84.5:factor(reg_name)Bretagne ***
## time:factor(ageClass)94.5:factor(reg_name)Bretagne **
## time:factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire
## time:factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire *
## time:factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire **
## time:factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire *
## time:factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire .
## time:factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire **
## time:factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire
## time:factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire
## time:factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire
## time:factor(ageClass)14.5:factor(reg_name)Corse ***
## time:factor(ageClass)24.5:factor(reg_name)Corse ***
## time:factor(ageClass)34.5:factor(reg_name)Corse ***
## time:factor(ageClass)44.5:factor(reg_name)Corse *
## time:factor(ageClass)54.5:factor(reg_name)Corse **
## time:factor(ageClass)64.5:factor(reg_name)Corse ***
## time:factor(ageClass)74.5:factor(reg_name)Corse ***
## time:factor(ageClass)84.5:factor(reg_name)Corse .
## time:factor(ageClass)94.5:factor(reg_name)Corse
## time:factor(ageClass)14.5:factor(reg_name)Grand Est ***
## time:factor(ageClass)24.5:factor(reg_name)Grand Est
## time:factor(ageClass)34.5:factor(reg_name)Grand Est
## time:factor(ageClass)44.5:factor(reg_name)Grand Est
## time:factor(ageClass)54.5:factor(reg_name)Grand Est
## time:factor(ageClass)64.5:factor(reg_name)Grand Est
## time:factor(ageClass)74.5:factor(reg_name)Grand Est
## time:factor(ageClass)84.5:factor(reg_name)Grand Est **
## time:factor(ageClass)94.5:factor(reg_name)Grand Est .
## time:factor(ageClass)14.5:factor(reg_name)Guadeloupe
## time:factor(ageClass)24.5:factor(reg_name)Guadeloupe
## time:factor(ageClass)34.5:factor(reg_name)Guadeloupe
## time:factor(ageClass)44.5:factor(reg_name)Guadeloupe
## time:factor(ageClass)54.5:factor(reg_name)Guadeloupe
## time:factor(ageClass)64.5:factor(reg_name)Guadeloupe
## time:factor(ageClass)74.5:factor(reg_name)Guadeloupe
## time:factor(ageClass)84.5:factor(reg_name)Guadeloupe
## time:factor(ageClass)94.5:factor(reg_name)Guadeloupe
## time:factor(ageClass)14.5:factor(reg_name)Guyane
## time:factor(ageClass)24.5:factor(reg_name)Guyane
## time:factor(ageClass)34.5:factor(reg_name)Guyane
## time:factor(ageClass)44.5:factor(reg_name)Guyane
## time:factor(ageClass)54.5:factor(reg_name)Guyane
## time:factor(ageClass)64.5:factor(reg_name)Guyane
## time:factor(ageClass)74.5:factor(reg_name)Guyane
## time:factor(ageClass)84.5:factor(reg_name)Guyane
## time:factor(ageClass)94.5:factor(reg_name)Guyane
## time:factor(ageClass)14.5:factor(reg_name)Hauts-de-France ***
## time:factor(ageClass)24.5:factor(reg_name)Hauts-de-France
## time:factor(ageClass)34.5:factor(reg_name)Hauts-de-France
## time:factor(ageClass)44.5:factor(reg_name)Hauts-de-France
## time:factor(ageClass)54.5:factor(reg_name)Hauts-de-France
## time:factor(ageClass)64.5:factor(reg_name)Hauts-de-France *
## time:factor(ageClass)74.5:factor(reg_name)Hauts-de-France *
## time:factor(ageClass)84.5:factor(reg_name)Hauts-de-France
## time:factor(ageClass)94.5:factor(reg_name)Hauts-de-France *
## time:factor(ageClass)14.5:factor(reg_name)ÃŽle-de-France
## time:factor(ageClass)24.5:factor(reg_name)ÃŽle-de-France *
## time:factor(ageClass)34.5:factor(reg_name)ÃŽle-de-France
## time:factor(ageClass)44.5:factor(reg_name)ÃŽle-de-France
## time:factor(ageClass)54.5:factor(reg_name)ÃŽle-de-France
## time:factor(ageClass)64.5:factor(reg_name)ÃŽle-de-France *
## time:factor(ageClass)74.5:factor(reg_name)ÃŽle-de-France
## time:factor(ageClass)84.5:factor(reg_name)ÃŽle-de-France ***
## time:factor(ageClass)94.5:factor(reg_name)ÃŽle-de-France ***
## time:factor(ageClass)14.5:factor(reg_name)La Réunion .
## time:factor(ageClass)24.5:factor(reg_name)La Réunion .
## time:factor(ageClass)34.5:factor(reg_name)La Réunion **
## time:factor(ageClass)44.5:factor(reg_name)La Réunion **
## time:factor(ageClass)54.5:factor(reg_name)La Réunion **
## time:factor(ageClass)64.5:factor(reg_name)La Réunion ***
## time:factor(ageClass)74.5:factor(reg_name)La Réunion ***
## time:factor(ageClass)84.5:factor(reg_name)La Réunion
## time:factor(ageClass)94.5:factor(reg_name)La Réunion
## time:factor(ageClass)14.5:factor(reg_name)Martinique
## time:factor(ageClass)24.5:factor(reg_name)Martinique
## time:factor(ageClass)34.5:factor(reg_name)Martinique .
## time:factor(ageClass)44.5:factor(reg_name)Martinique
## time:factor(ageClass)54.5:factor(reg_name)Martinique .
## time:factor(ageClass)64.5:factor(reg_name)Martinique
## time:factor(ageClass)74.5:factor(reg_name)Martinique **
## time:factor(ageClass)84.5:factor(reg_name)Martinique .
## time:factor(ageClass)94.5:factor(reg_name)Martinique
## time:factor(ageClass)14.5:factor(reg_name)Mayotte
## time:factor(ageClass)24.5:factor(reg_name)Mayotte
## time:factor(ageClass)34.5:factor(reg_name)Mayotte
## time:factor(ageClass)44.5:factor(reg_name)Mayotte
## time:factor(ageClass)54.5:factor(reg_name)Mayotte
## time:factor(ageClass)64.5:factor(reg_name)Mayotte
## time:factor(ageClass)74.5:factor(reg_name)Mayotte
## time:factor(ageClass)84.5:factor(reg_name)Mayotte
## time:factor(ageClass)94.5:factor(reg_name)Mayotte
## time:factor(ageClass)14.5:factor(reg_name)Normandie ***
## time:factor(ageClass)24.5:factor(reg_name)Normandie
## time:factor(ageClass)34.5:factor(reg_name)Normandie ***
## time:factor(ageClass)44.5:factor(reg_name)Normandie
## time:factor(ageClass)54.5:factor(reg_name)Normandie
## time:factor(ageClass)64.5:factor(reg_name)Normandie *
## time:factor(ageClass)74.5:factor(reg_name)Normandie
## time:factor(ageClass)84.5:factor(reg_name)Normandie ***
## time:factor(ageClass)94.5:factor(reg_name)Normandie ***
## time:factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine ***
## time:factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine ***
## time:factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine ***
## time:factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine *
## time:factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine ***
## time:factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine
## time:factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine *
## time:factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine ***
## time:factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine **
## time:factor(ageClass)14.5:factor(reg_name)Occitanie
## time:factor(ageClass)24.5:factor(reg_name)Occitanie
## time:factor(ageClass)34.5:factor(reg_name)Occitanie
## time:factor(ageClass)44.5:factor(reg_name)Occitanie
## time:factor(ageClass)54.5:factor(reg_name)Occitanie
## time:factor(ageClass)64.5:factor(reg_name)Occitanie *
## time:factor(ageClass)74.5:factor(reg_name)Occitanie *
## time:factor(ageClass)84.5:factor(reg_name)Occitanie
## time:factor(ageClass)94.5:factor(reg_name)Occitanie ***
## time:factor(ageClass)14.5:factor(reg_name)Pays de la Loire
## time:factor(ageClass)24.5:factor(reg_name)Pays de la Loire
## time:factor(ageClass)34.5:factor(reg_name)Pays de la Loire
## time:factor(ageClass)44.5:factor(reg_name)Pays de la Loire .
## time:factor(ageClass)54.5:factor(reg_name)Pays de la Loire
## time:factor(ageClass)64.5:factor(reg_name)Pays de la Loire **
## time:factor(ageClass)74.5:factor(reg_name)Pays de la Loire .
## time:factor(ageClass)84.5:factor(reg_name)Pays de la Loire *
## time:factor(ageClass)94.5:factor(reg_name)Pays de la Loire ***
## time:factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur ***
## time:factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur
## time:factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur
## time:factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur
## time:factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur
## time:factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur
## time:factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur **
## time:factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur ***
## time:factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 113412.0 on 3049 degrees of freedom
## Residual deviance: 2246.2 on 2701 degrees of freedom
## (540 observations deleted due to missingness)
## AIC: 18927
##
## Number of Fisher Scoring iterations: 17
# Without interaction
mdl1 <- glm(cbind(V1, notV1) ~ time*factor(reg_name) + factor(ageClass), data = dat.regions.ages, family = "binomial")
summary(mdl1)
##
## Call:
## glm(formula = cbind(V1, notV1) ~ time * factor(reg_name) + factor(ageClass),
## family = "binomial", data = dat.regions.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -6.5584 -0.7909 0.0000 0.8827 5.0948
##
## Coefficients:
## Estimate Std. Error z value
## (Intercept) -2.947e-01 1.169e-02 -25.203
## time 5.735e-02 9.192e-04 62.386
## factor(reg_name)Bourgogne-Franche-Comté -5.194e-01 1.936e-02 -26.825
## factor(reg_name)Bretagne 5.714e-01 1.995e-02 28.634
## factor(reg_name)Centre-Val de Loire 9.113e-02 2.058e-02 4.428
## factor(reg_name)Corse 1.130e+00 6.151e-02 18.370
## factor(reg_name)Grand Est -5.024e-01 1.493e-02 -33.651
## factor(reg_name)Guadeloupe 9.994e-01 1.437e-01 6.954
## factor(reg_name)Guyane -9.876e-01 2.583e-01 -3.824
## factor(reg_name)Hauts-de-France 5.846e-01 1.204e-02 48.561
## factor(reg_name)ÃŽle-de-France 6.461e-01 1.109e-02 58.283
## factor(reg_name)La Réunion -1.960e+00 9.085e-02 -21.573
## factor(reg_name)Martinique 4.160e-01 1.295e-01 3.213
## factor(reg_name)Mayotte -5.280e+00 4.552e-01 -11.601
## factor(reg_name)Normandie -3.531e-02 1.802e-02 -1.959
## factor(reg_name)Nouvelle-Aquitaine -4.575e-02 1.681e-02 -2.722
## factor(reg_name)Occitanie 3.266e-01 1.428e-02 22.881
## factor(reg_name)Pays de la Loire 1.516e-02 1.675e-02 0.905
## factor(reg_name)Provence-Alpes-Côte d'Azur 3.144e-01 1.255e-02 25.055
## factor(ageClass)14.5 -5.841e-02 8.685e-03 -6.725
## factor(ageClass)24.5 -1.115e-01 8.548e-03 -13.042
## factor(ageClass)34.5 -8.241e-02 8.554e-03 -9.634
## factor(ageClass)44.5 -7.708e-02 8.543e-03 -9.023
## factor(ageClass)54.5 -1.583e-01 8.609e-03 -18.393
## factor(ageClass)64.5 -2.466e-01 9.005e-03 -27.389
## factor(ageClass)74.5 -4.342e-01 9.722e-03 -44.662
## factor(ageClass)84.5 -7.102e-01 1.056e-02 -67.231
## factor(ageClass)94.5 -8.899e-01 1.322e-02 -67.296
## time:factor(reg_name)Bourgogne-Franche-Comté 9.398e-03 1.919e-03 4.898
## time:factor(reg_name)Bretagne -1.462e-03 2.071e-03 -0.706
## time:factor(reg_name)Centre-Val de Loire -4.587e-06 2.014e-03 -0.002
## time:factor(reg_name)Corse -1.819e-02 6.189e-03 -2.940
## time:factor(reg_name)Grand Est 2.785e-03 1.466e-03 1.900
## time:factor(reg_name)Guadeloupe 5.792e-02 1.459e-02 3.970
## time:factor(reg_name)Guyane 5.869e-02 2.767e-02 2.121
## time:factor(reg_name)Hauts-de-France -1.037e-02 1.220e-03 -8.506
## time:factor(reg_name)ÃŽle-de-France -2.095e-02 1.116e-03 -18.771
## time:factor(reg_name)La Réunion -7.881e-02 8.551e-03 -9.216
## time:factor(reg_name)Martinique 1.169e-02 1.310e-02 0.893
## time:factor(reg_name)Mayotte 2.725e-02 4.174e-02 0.653
## time:factor(reg_name)Normandie 1.865e-02 1.800e-03 10.361
## time:factor(reg_name)Nouvelle-Aquitaine 6.240e-03 1.700e-03 3.669
## time:factor(reg_name)Occitanie -1.887e-03 1.456e-03 -1.296
## time:factor(reg_name)Pays de la Loire -5.600e-03 1.683e-03 -3.327
## time:factor(reg_name)Provence-Alpes-Côte d'Azur 1.672e-02 1.302e-03 12.844
## Pr(>|z|)
## (Intercept) < 2e-16 ***
## time < 2e-16 ***
## factor(reg_name)Bourgogne-Franche-Comté < 2e-16 ***
## factor(reg_name)Bretagne < 2e-16 ***
## factor(reg_name)Centre-Val de Loire 9.50e-06 ***
## factor(reg_name)Corse < 2e-16 ***
## factor(reg_name)Grand Est < 2e-16 ***
## factor(reg_name)Guadeloupe 3.55e-12 ***
## factor(reg_name)Guyane 0.000131 ***
## factor(reg_name)Hauts-de-France < 2e-16 ***
## factor(reg_name)ÃŽle-de-France < 2e-16 ***
## factor(reg_name)La Réunion < 2e-16 ***
## factor(reg_name)Martinique 0.001312 **
## factor(reg_name)Mayotte < 2e-16 ***
## factor(reg_name)Normandie 0.050128 .
## factor(reg_name)Nouvelle-Aquitaine 0.006491 **
## factor(reg_name)Occitanie < 2e-16 ***
## factor(reg_name)Pays de la Loire 0.365481
## factor(reg_name)Provence-Alpes-Côte d'Azur < 2e-16 ***
## factor(ageClass)14.5 1.75e-11 ***
## factor(ageClass)24.5 < 2e-16 ***
## factor(ageClass)34.5 < 2e-16 ***
## factor(ageClass)44.5 < 2e-16 ***
## factor(ageClass)54.5 < 2e-16 ***
## factor(ageClass)64.5 < 2e-16 ***
## factor(ageClass)74.5 < 2e-16 ***
## factor(ageClass)84.5 < 2e-16 ***
## factor(ageClass)94.5 < 2e-16 ***
## time:factor(reg_name)Bourgogne-Franche-Comté 9.69e-07 ***
## time:factor(reg_name)Bretagne 0.480353
## time:factor(reg_name)Centre-Val de Loire 0.998183
## time:factor(reg_name)Corse 0.003286 **
## time:factor(reg_name)Grand Est 0.057442 .
## time:factor(reg_name)Guadeloupe 7.19e-05 ***
## time:factor(reg_name)Guyane 0.033920 *
## time:factor(reg_name)Hauts-de-France < 2e-16 ***
## time:factor(reg_name)ÃŽle-de-France < 2e-16 ***
## time:factor(reg_name)La Réunion < 2e-16 ***
## time:factor(reg_name)Martinique 0.371936
## time:factor(reg_name)Mayotte 0.513930
## time:factor(reg_name)Normandie < 2e-16 ***
## time:factor(reg_name)Nouvelle-Aquitaine 0.000243 ***
## time:factor(reg_name)Occitanie 0.194864
## time:factor(reg_name)Pays de la Loire 0.000877 ***
## time:factor(reg_name)Provence-Alpes-Côte d'Azur < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 113412.0 on 3049 degrees of freedom
## Residual deviance: 6054.6 on 3005 degrees of freedom
## (540 observations deleted due to missingness)
## AIC: 22128
##
## Number of Fisher Scoring iterations: 6
# Without interaction
mdl1bis <- glm(cbind(V1, notV1) ~ time*factor(ageClass) + factor(reg_name), data = dat.regions.ages, family = "binomial")
summary(mdl1bis)
##
## Call:
## glm(formula = cbind(V1, notV1) ~ time * factor(ageClass) + factor(reg_name),
## family = "binomial", data = dat.regions.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -6.0968 -0.9147 0.0000 0.9812 7.4498
##
## Coefficients:
## Estimate Std. Error z value
## (Intercept) -0.170794 0.015381 -11.105
## time 0.042839 0.001475 29.041
## factor(ageClass)14.5 -0.127467 0.017022 -7.488
## factor(ageClass)24.5 -0.214189 0.016773 -12.770
## factor(ageClass)34.5 -0.145865 0.016735 -8.716
## factor(ageClass)44.5 -0.143081 0.016709 -8.563
## factor(ageClass)54.5 -0.251776 0.016875 -14.920
## factor(ageClass)64.5 -0.340223 0.017704 -19.217
## factor(ageClass)74.5 -0.650177 0.019228 -33.814
## factor(ageClass)84.5 -0.918696 0.020638 -44.515
## factor(ageClass)94.5 -1.053709 0.025276 -41.688
## factor(reg_name)Bourgogne-Franche-Comté -0.435910 0.009565 -45.572
## factor(reg_name)Bretagne 0.557710 0.010378 53.740
## factor(reg_name)Centre-Val de Loire 0.091897 0.010157 9.047
## factor(reg_name)Corse 0.973375 0.031223 31.175
## factor(reg_name)Grand Est -0.475638 0.007314 -65.028
## factor(reg_name)Guadeloupe 1.524675 0.068491 22.261
## factor(reg_name)Guyane -0.535538 0.133505 -4.011
## factor(reg_name)Hauts-de-France 0.495943 0.006125 80.966
## factor(reg_name)ÃŽle-de-France 0.465823 0.005624 82.834
## factor(reg_name)La Réunion -2.754360 0.042107 -65.413
## factor(reg_name)Martinique 0.518608 0.061566 8.424
## factor(reg_name)Mayotte -5.022954 0.204737 -24.534
## factor(reg_name)Normandie 0.127488 0.008934 14.270
## factor(reg_name)Nouvelle-Aquitaine 0.007811 0.008468 0.922
## factor(reg_name)Occitanie 0.311201 0.007375 42.199
## factor(reg_name)Pays de la Loire -0.032831 0.008538 -3.845
## factor(reg_name)Provence-Alpes-Côte d'Azur 0.446784 0.006487 68.876
## time:factor(ageClass)14.5 0.008044 0.001702 4.727
## time:factor(ageClass)24.5 0.012047 0.001677 7.186
## time:factor(ageClass)34.5 0.007343 0.001676 4.381
## time:factor(ageClass)44.5 0.007737 0.001675 4.618
## time:factor(ageClass)54.5 0.011021 0.001691 6.518
## time:factor(ageClass)64.5 0.011005 0.001769 6.220
## time:factor(ageClass)74.5 0.025182 0.001923 13.097
## time:factor(ageClass)84.5 0.024747 0.002089 11.846
## time:factor(ageClass)94.5 0.019538 0.002628 7.433
## Pr(>|z|)
## (Intercept) < 2e-16 ***
## time < 2e-16 ***
## factor(ageClass)14.5 6.98e-14 ***
## factor(ageClass)24.5 < 2e-16 ***
## factor(ageClass)34.5 < 2e-16 ***
## factor(ageClass)44.5 < 2e-16 ***
## factor(ageClass)54.5 < 2e-16 ***
## factor(ageClass)64.5 < 2e-16 ***
## factor(ageClass)74.5 < 2e-16 ***
## factor(ageClass)84.5 < 2e-16 ***
## factor(ageClass)94.5 < 2e-16 ***
## factor(reg_name)Bourgogne-Franche-Comté < 2e-16 ***
## factor(reg_name)Bretagne < 2e-16 ***
## factor(reg_name)Centre-Val de Loire < 2e-16 ***
## factor(reg_name)Corse < 2e-16 ***
## factor(reg_name)Grand Est < 2e-16 ***
## factor(reg_name)Guadeloupe < 2e-16 ***
## factor(reg_name)Guyane 6.04e-05 ***
## factor(reg_name)Hauts-de-France < 2e-16 ***
## factor(reg_name)ÃŽle-de-France < 2e-16 ***
## factor(reg_name)La Réunion < 2e-16 ***
## factor(reg_name)Martinique < 2e-16 ***
## factor(reg_name)Mayotte < 2e-16 ***
## factor(reg_name)Normandie < 2e-16 ***
## factor(reg_name)Nouvelle-Aquitaine 0.35635
## factor(reg_name)Occitanie < 2e-16 ***
## factor(reg_name)Pays de la Loire 0.00012 ***
## factor(reg_name)Provence-Alpes-Côte d'Azur < 2e-16 ***
## time:factor(ageClass)14.5 2.27e-06 ***
## time:factor(ageClass)24.5 6.69e-13 ***
## time:factor(ageClass)34.5 1.18e-05 ***
## time:factor(ageClass)44.5 3.87e-06 ***
## time:factor(ageClass)54.5 7.13e-11 ***
## time:factor(ageClass)64.5 4.97e-10 ***
## time:factor(ageClass)74.5 < 2e-16 ***
## time:factor(ageClass)84.5 < 2e-16 ***
## time:factor(ageClass)94.5 1.06e-13 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 113412.0 on 3049 degrees of freedom
## Residual deviance: 7502.1 on 3013 degrees of freedom
## (540 observations deleted due to missingness)
## AIC: 23559
##
## Number of Fisher Scoring iterations: 5
# Without interaction at all
mdl2 <- glm(cbind(V1, notV1) ~ time + factor(ageClass) + factor(reg_name), data = dat.regions.ages, family = "binomial")
summary(mdl2)
##
## Call:
## glm(formula = cbind(V1, notV1) ~ time + factor(ageClass) + factor(reg_name),
## family = "binomial", data = dat.regions.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -7.2722 -0.8808 0.0000 0.9799 8.0354
##
## Coefficients:
## Estimate Std. Error z value
## (Intercept) -0.2648359 0.0090584 -29.236
## time 0.0537605 0.0003101 173.364
## factor(ageClass)14.5 -0.0583640 0.0086809 -6.723
## factor(ageClass)24.5 -0.1106522 0.0085445 -12.950
## factor(ageClass)34.5 -0.0823989 0.0085504 -9.637
## factor(ageClass)44.5 -0.0761394 0.0085391 -8.917
## factor(ageClass)54.5 -0.1570956 0.0086044 -18.258
## factor(ageClass)64.5 -0.2456723 0.0089999 -27.297
## factor(ageClass)74.5 -0.4330799 0.0097156 -44.576
## factor(ageClass)84.5 -0.7096711 0.0105554 -67.233
## factor(ageClass)94.5 -0.8911538 0.0132095 -67.463
## factor(reg_name)Bourgogne-Franche-Comté -0.4356291 0.0095640 -45.549
## factor(reg_name)Bretagne 0.5582156 0.0103751 53.803
## factor(reg_name)Centre-Val de Loire 0.0927682 0.0101556 9.135
## factor(reg_name)Corse 0.9752876 0.0312132 31.246
## factor(reg_name)Grand Est -0.4750509 0.0073146 -64.945
## factor(reg_name)Guadeloupe 1.5243190 0.0684935 22.255
## factor(reg_name)Guyane -0.5351203 0.1335890 -4.006
## factor(reg_name)Hauts-de-France 0.4966018 0.0061247 81.082
## factor(reg_name)ÃŽle-de-France 0.4659388 0.0056232 82.860
## factor(reg_name)La Réunion -2.7567557 0.0421142 -65.459
## factor(reg_name)Martinique 0.5188033 0.0615424 8.430
## factor(reg_name)Mayotte -5.0225215 0.2047367 -24.532
## factor(reg_name)Normandie 0.1288819 0.0089326 14.428
## factor(reg_name)Nouvelle-Aquitaine 0.0076666 0.0084674 0.905
## factor(reg_name)Occitanie 0.3102706 0.0073722 42.086
## factor(reg_name)Pays de la Loire -0.0326336 0.0085370 -3.823
## factor(reg_name)Provence-Alpes-Côte d'Azur 0.4467034 0.0064850 68.883
## Pr(>|z|)
## (Intercept) < 2e-16 ***
## time < 2e-16 ***
## factor(ageClass)14.5 1.78e-11 ***
## factor(ageClass)24.5 < 2e-16 ***
## factor(ageClass)34.5 < 2e-16 ***
## factor(ageClass)44.5 < 2e-16 ***
## factor(ageClass)54.5 < 2e-16 ***
## factor(ageClass)64.5 < 2e-16 ***
## factor(ageClass)74.5 < 2e-16 ***
## factor(ageClass)84.5 < 2e-16 ***
## factor(ageClass)94.5 < 2e-16 ***
## factor(reg_name)Bourgogne-Franche-Comté < 2e-16 ***
## factor(reg_name)Bretagne < 2e-16 ***
## factor(reg_name)Centre-Val de Loire < 2e-16 ***
## factor(reg_name)Corse < 2e-16 ***
## factor(reg_name)Grand Est < 2e-16 ***
## factor(reg_name)Guadeloupe < 2e-16 ***
## factor(reg_name)Guyane 6.18e-05 ***
## factor(reg_name)Hauts-de-France < 2e-16 ***
## factor(reg_name)ÃŽle-de-France < 2e-16 ***
## factor(reg_name)La Réunion < 2e-16 ***
## factor(reg_name)Martinique < 2e-16 ***
## factor(reg_name)Mayotte < 2e-16 ***
## factor(reg_name)Normandie < 2e-16 ***
## factor(reg_name)Nouvelle-Aquitaine 0.365235
## factor(reg_name)Occitanie < 2e-16 ***
## factor(reg_name)Pays de la Loire 0.000132 ***
## factor(reg_name)Provence-Alpes-Côte d'Azur < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 113412.0 on 3049 degrees of freedom
## Residual deviance: 7844.6 on 3022 degrees of freedom
## (540 observations deleted due to missingness)
## AIC: 23884
##
## Number of Fisher Scoring iterations: 5
## Likelihood ratio tests
anova(mdl1, mdl0, test="Chisq")
## Analysis of Deviance Table
##
## Model 1: cbind(V1, notV1) ~ time * factor(reg_name) + factor(ageClass)
## Model 2: cbind(V1, notV1) ~ time * factor(ageClass) * factor(reg_name)
## Resid. Df Resid. Dev Df Deviance Pr(>Chi)
## 1 3005 6054.6
## 2 2701 2246.2 304 3808.4 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
anova(mdl1bis, mdl0, test="Chisq")
## Analysis of Deviance Table
##
## Model 1: cbind(V1, notV1) ~ time * factor(ageClass) + factor(reg_name)
## Model 2: cbind(V1, notV1) ~ time * factor(ageClass) * factor(reg_name)
## Resid. Df Resid. Dev Df Deviance Pr(>Chi)
## 1 3013 7502.1
## 2 2701 2246.2 312 5255.8 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
anova(mdl2, mdl0, test="Chisq")
## Analysis of Deviance Table
##
## Model 1: cbind(V1, notV1) ~ time + factor(ageClass) + factor(reg_name)
## Model 2: cbind(V1, notV1) ~ time * factor(ageClass) * factor(reg_name)
## Resid. Df Resid. Dev Df Deviance Pr(>Chi)
## 1 3022 7844.6
## 2 2701 2246.2 321 5598.4 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
mdl3 <- glm(cbind(V1, notV1) ~ time * ageClass * factor(reg_name), data = dat.regions.ages, family = "binomial")
summary(mdl3)
##
## Call:
## glm(formula = cbind(V1, notV1) ~ time * ageClass * factor(reg_name),
## family = "binomial", data = dat.regions.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -9.3444 -1.1485 -0.0175 0.8235 7.6969
##
## Coefficients:
## Estimate Std. Error
## (Intercept) 6.899e-03 1.937e-02
## time 4.310e-02 1.961e-03
## ageClass -1.126e-02 4.034e-04
## factor(reg_name)Bourgogne-Franche-Comté -5.871e-01 4.152e-02
## factor(reg_name)Bretagne 3.933e-01 4.125e-02
## factor(reg_name)Centre-Val de Loire 6.498e-02 4.448e-02
## factor(reg_name)Corse 4.198e-01 1.458e-01
## factor(reg_name)Grand Est -7.690e-01 3.106e-02
## factor(reg_name)Guadeloupe 1.823e-01 3.723e-01
## factor(reg_name)Guyane -1.799e+00 5.600e-01
## factor(reg_name)Hauts-de-France 3.263e-01 2.569e-02
## factor(reg_name)ÃŽle-de-France 5.480e-01 2.394e-02
## factor(reg_name)La Réunion -3.337e+00 2.179e-01
## factor(reg_name)Martinique 9.231e-01 3.251e-01
## factor(reg_name)Mayotte -1.494e+01 1.065e+01
## factor(reg_name)Normandie -1.743e-01 3.837e-02
## factor(reg_name)Nouvelle-Aquitaine 7.943e-02 3.586e-02
## factor(reg_name)Occitanie 2.055e-01 3.067e-02
## factor(reg_name)Pays de la Loire -3.367e-01 3.518e-02
## factor(reg_name)Provence-Alpes-Côte d'Azur 3.529e-01 2.734e-02
## time:ageClass 3.390e-04 4.113e-05
## time:factor(reg_name)Bourgogne-Franche-Comté 1.083e-02 4.121e-03
## time:factor(reg_name)Bretagne 1.518e-03 4.269e-03
## time:factor(reg_name)Centre-Val de Loire -4.705e-04 4.364e-03
## time:factor(reg_name)Corse -1.260e-03 1.412e-02
## time:factor(reg_name)Grand Est 1.575e-02 3.080e-03
## time:factor(reg_name)Guadeloupe 1.796e-01 3.950e-02
## time:factor(reg_name)Guyane -1.025e-01 6.655e-02
## time:factor(reg_name)Hauts-de-France 7.519e-03 2.607e-03
## time:factor(reg_name)ÃŽle-de-France -2.028e-02 2.409e-03
## time:factor(reg_name)La Réunion 3.157e-02 1.937e-02
## time:factor(reg_name)Martinique -2.597e-02 3.306e-02
## time:factor(reg_name)Mayotte -8.621e-01 1.114e+00
## time:factor(reg_name)Normandie 2.664e-02 3.866e-03
## time:factor(reg_name)Nouvelle-Aquitaine 9.780e-03 3.626e-03
## time:factor(reg_name)Occitanie 1.077e-02 3.115e-03
## time:factor(reg_name)Pays de la Loire 2.053e-02 3.532e-03
## time:factor(reg_name)Provence-Alpes-Côte d'Azur 1.161e-02 2.851e-03
## ageClass:factor(reg_name)Bourgogne-Franche-Comté 1.635e-03 8.394e-04
## ageClass:factor(reg_name)Bretagne 3.954e-03 8.715e-04
## ageClass:factor(reg_name)Centre-Val de Loire 6.892e-04 8.860e-04
## ageClass:factor(reg_name)Corse 1.605e-02 2.930e-03
## ageClass:factor(reg_name)Grand Est 6.289e-03 6.565e-04
## ageClass:factor(reg_name)Guadeloupe 1.925e-02 7.856e-03
## ageClass:factor(reg_name)Guyane 1.802e-02 1.406e-02
## ageClass:factor(reg_name)Hauts-de-France 6.174e-03 5.372e-04
## ageClass:factor(reg_name)ÃŽle-de-France 2.469e-03 5.038e-04
## ageClass:factor(reg_name)La Réunion 3.601e-02 4.814e-03
## ageClass:factor(reg_name)Martinique -1.002e-02 6.184e-03
## ageClass:factor(reg_name)Mayotte 1.542e-01 1.638e-01
## ageClass:factor(reg_name)Normandie 3.354e-03 7.927e-04
## ageClass:factor(reg_name)Nouvelle-Aquitaine -2.962e-03 7.447e-04
## ageClass:factor(reg_name)Occitanie 2.731e-03 6.160e-04
## ageClass:factor(reg_name)Pays de la Loire 8.164e-03 7.280e-04
## ageClass:factor(reg_name)Provence-Alpes-Côte d'Azur -6.298e-04 5.549e-04
## time:ageClass:factor(reg_name)Bourgogne-Franche-Comté -3.898e-05 8.417e-05
## time:ageClass:factor(reg_name)Bretagne -4.990e-05 9.166e-05
## time:ageClass:factor(reg_name)Centre-Val de Loire -3.791e-06 8.731e-05
## time:ageClass:factor(reg_name)Corse -4.225e-04 2.865e-04
## time:ageClass:factor(reg_name)Grand Est -2.987e-04 6.509e-05
## time:ageClass:factor(reg_name)Guadeloupe -2.722e-03 7.998e-04
## time:ageClass:factor(reg_name)Guyane 5.851e-03 1.867e-03
## time:ageClass:factor(reg_name)Hauts-de-France -4.244e-04 5.474e-05
## time:ageClass:factor(reg_name)ÃŽle-de-France -4.709e-06 5.108e-05
## time:ageClass:factor(reg_name)La Réunion -2.889e-03 4.523e-04
## time:ageClass:factor(reg_name)Martinique 7.214e-04 6.154e-04
## time:ageClass:factor(reg_name)Mayotte 1.309e-02 1.714e-02
## time:ageClass:factor(reg_name)Normandie -1.967e-04 7.929e-05
## time:ageClass:factor(reg_name)Nouvelle-Aquitaine -8.710e-05 7.549e-05
## time:ageClass:factor(reg_name)Occitanie -2.941e-04 6.364e-05
## time:ageClass:factor(reg_name)Pays de la Loire -6.167e-04 7.391e-05
## time:ageClass:factor(reg_name)Provence-Alpes-Côte d'Azur 1.017e-04 5.817e-05
## z value Pr(>|z|)
## (Intercept) 0.356 0.721766
## time 21.977 < 2e-16 ***
## ageClass -27.915 < 2e-16 ***
## factor(reg_name)Bourgogne-Franche-Comté -14.139 < 2e-16 ***
## factor(reg_name)Bretagne 9.535 < 2e-16 ***
## factor(reg_name)Centre-Val de Loire 1.461 0.144025
## factor(reg_name)Corse 2.879 0.003987 **
## factor(reg_name)Grand Est -24.756 < 2e-16 ***
## factor(reg_name)Guadeloupe 0.490 0.624305
## factor(reg_name)Guyane -3.213 0.001315 **
## factor(reg_name)Hauts-de-France 12.700 < 2e-16 ***
## factor(reg_name)ÃŽle-de-France 22.889 < 2e-16 ***
## factor(reg_name)La Réunion -15.315 < 2e-16 ***
## factor(reg_name)Martinique 2.840 0.004514 **
## factor(reg_name)Mayotte -1.402 0.160786
## factor(reg_name)Normandie -4.544 5.53e-06 ***
## factor(reg_name)Nouvelle-Aquitaine 2.215 0.026757 *
## factor(reg_name)Occitanie 6.700 2.08e-11 ***
## factor(reg_name)Pays de la Loire -9.572 < 2e-16 ***
## factor(reg_name)Provence-Alpes-Côte d'Azur 12.906 < 2e-16 ***
## time:ageClass 8.242 < 2e-16 ***
## time:factor(reg_name)Bourgogne-Franche-Comté 2.627 0.008604 **
## time:factor(reg_name)Bretagne 0.355 0.722236
## time:factor(reg_name)Centre-Val de Loire -0.108 0.914152
## time:factor(reg_name)Corse -0.089 0.928897
## time:factor(reg_name)Grand Est 5.112 3.19e-07 ***
## time:factor(reg_name)Guadeloupe 4.547 5.43e-06 ***
## time:factor(reg_name)Guyane -1.540 0.123664
## time:factor(reg_name)Hauts-de-France 2.884 0.003925 **
## time:factor(reg_name)ÃŽle-de-France -8.420 < 2e-16 ***
## time:factor(reg_name)La Réunion 1.630 0.103121
## time:factor(reg_name)Martinique -0.785 0.432169
## time:factor(reg_name)Mayotte -0.774 0.439116
## time:factor(reg_name)Normandie 6.891 5.53e-12 ***
## time:factor(reg_name)Nouvelle-Aquitaine 2.697 0.006996 **
## time:factor(reg_name)Occitanie 3.457 0.000547 ***
## time:factor(reg_name)Pays de la Loire 5.812 6.18e-09 ***
## time:factor(reg_name)Provence-Alpes-Côte d'Azur 4.073 4.64e-05 ***
## ageClass:factor(reg_name)Bourgogne-Franche-Comté 1.948 0.051402 .
## ageClass:factor(reg_name)Bretagne 4.537 5.71e-06 ***
## ageClass:factor(reg_name)Centre-Val de Loire 0.778 0.436652
## ageClass:factor(reg_name)Corse 5.477 4.34e-08 ***
## ageClass:factor(reg_name)Grand Est 9.579 < 2e-16 ***
## ageClass:factor(reg_name)Guadeloupe 2.451 0.014255 *
## ageClass:factor(reg_name)Guyane 1.281 0.200064
## ageClass:factor(reg_name)Hauts-de-France 11.493 < 2e-16 ***
## ageClass:factor(reg_name)ÃŽle-de-France 4.901 9.54e-07 ***
## ageClass:factor(reg_name)La Réunion 7.480 7.42e-14 ***
## ageClass:factor(reg_name)Martinique -1.620 0.105231
## ageClass:factor(reg_name)Mayotte 0.941 0.346479
## ageClass:factor(reg_name)Normandie 4.231 2.33e-05 ***
## ageClass:factor(reg_name)Nouvelle-Aquitaine -3.977 6.97e-05 ***
## ageClass:factor(reg_name)Occitanie 4.434 9.24e-06 ***
## ageClass:factor(reg_name)Pays de la Loire 11.213 < 2e-16 ***
## ageClass:factor(reg_name)Provence-Alpes-Côte d'Azur -1.135 0.256423
## time:ageClass:factor(reg_name)Bourgogne-Franche-Comté -0.463 0.643256
## time:ageClass:factor(reg_name)Bretagne -0.544 0.586162
## time:ageClass:factor(reg_name)Centre-Val de Loire -0.043 0.965364
## time:ageClass:factor(reg_name)Corse -1.475 0.140337
## time:ageClass:factor(reg_name)Grand Est -4.590 4.44e-06 ***
## time:ageClass:factor(reg_name)Guadeloupe -3.403 0.000666 ***
## time:ageClass:factor(reg_name)Guyane 3.134 0.001723 **
## time:ageClass:factor(reg_name)Hauts-de-France -7.754 8.92e-15 ***
## time:ageClass:factor(reg_name)ÃŽle-de-France -0.092 0.926550
## time:ageClass:factor(reg_name)La Réunion -6.386 1.70e-10 ***
## time:ageClass:factor(reg_name)Martinique 1.172 0.241101
## time:ageClass:factor(reg_name)Mayotte 0.764 0.445095
## time:ageClass:factor(reg_name)Normandie -2.480 0.013120 *
## time:ageClass:factor(reg_name)Nouvelle-Aquitaine -1.154 0.248562
## time:ageClass:factor(reg_name)Occitanie -4.621 3.81e-06 ***
## time:ageClass:factor(reg_name)Pays de la Loire -8.344 < 2e-16 ***
## time:ageClass:factor(reg_name)Provence-Alpes-Côte d'Azur 1.748 0.080522 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 113412.0 on 3049 degrees of freedom
## Residual deviance: 9428.9 on 2978 degrees of freedom
## (540 observations deleted due to missingness)
## AIC: 25556
##
## Number of Fisher Scoring iterations: 8
## Likelihood ratio test
anova(mdl3, mdl0, test="Chisq")
## Analysis of Deviance Table
##
## Model 1: cbind(V1, notV1) ~ time * ageClass * factor(reg_name)
## Model 2: cbind(V1, notV1) ~ time * factor(ageClass) * factor(reg_name)
## Resid. Df Resid. Dev Df Deviance Pr(>Chi)
## 1 2978 9428.9
## 2 2701 2246.2 277 7182.7 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# GLM
# Assuming that all IND (indetermine) are non-V1
mdl <- glm(cbind(V1, notV1) ~ date2 * as.factor(ageClass) + reg_name.fac, data = dat.regions.ages, family = "binomial")
summary(mdl)
##
## Call:
## glm(formula = cbind(V1, notV1) ~ date2 * as.factor(ageClass) +
## reg_name.fac, family = "binomial", data = dat.regions.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -6.0968 -0.9147 0.0000 0.9812 7.4498
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -8.002e+02 2.756e+01 -29.034 < 2e-16
## date2 4.284e-02 1.475e-03 29.041 < 2e-16
## as.factor(ageClass)14.5 -1.504e+02 3.179e+01 -4.729 2.25e-06
## as.factor(ageClass)24.5 -2.252e+02 3.132e+01 -7.189 6.52e-13
## as.factor(ageClass)34.5 -1.373e+02 3.132e+01 -4.383 1.17e-05
## as.factor(ageClass)44.5 -1.446e+02 3.130e+01 -4.621 3.83e-06
## as.factor(ageClass)54.5 -2.061e+02 3.159e+01 -6.523 6.90e-11
## as.factor(ageClass)64.5 -2.059e+02 3.306e+01 -6.228 4.74e-10
## as.factor(ageClass)74.5 -4.709e+02 3.593e+01 -13.109 < 2e-16
## as.factor(ageClass)84.5 -4.631e+02 3.903e+01 -11.864 < 2e-16
## as.factor(ageClass)94.5 -3.659e+02 4.911e+01 -7.451 9.23e-14
## reg_name.facBourgogne-Franche-Comté -4.359e-01 9.565e-03 -45.572 < 2e-16
## reg_name.facBretagne 5.577e-01 1.038e-02 53.740 < 2e-16
## reg_name.facCentre-Val de Loire 9.190e-02 1.016e-02 9.047 < 2e-16
## reg_name.facCorse 9.734e-01 3.122e-02 31.175 < 2e-16
## reg_name.facGrand Est -4.756e-01 7.314e-03 -65.028 < 2e-16
## reg_name.facGuadeloupe 1.525e+00 6.849e-02 22.261 < 2e-16
## reg_name.facGuyane -5.355e-01 1.335e-01 -4.011 6.04e-05
## reg_name.facHauts-de-France 4.959e-01 6.125e-03 80.966 < 2e-16
## reg_name.facÃŽle-de-France 4.658e-01 5.624e-03 82.834 < 2e-16
## reg_name.facLa Réunion -2.754e+00 4.211e-02 -65.413 < 2e-16
## reg_name.facMartinique 5.186e-01 6.157e-02 8.424 < 2e-16
## reg_name.facMayotte -5.023e+00 2.047e-01 -24.534 < 2e-16
## reg_name.facNormandie 1.275e-01 8.934e-03 14.270 < 2e-16
## reg_name.facNouvelle-Aquitaine 7.811e-03 8.468e-03 0.922 0.35635
## reg_name.facOccitanie 3.112e-01 7.375e-03 42.199 < 2e-16
## reg_name.facPays de la Loire -3.283e-02 8.538e-03 -3.845 0.00012
## reg_name.facProvence-Alpes-Côte d'Azur 4.468e-01 6.487e-03 68.876 < 2e-16
## date2:as.factor(ageClass)14.5 8.044e-03 1.702e-03 4.727 2.27e-06
## date2:as.factor(ageClass)24.5 1.205e-02 1.677e-03 7.186 6.69e-13
## date2:as.factor(ageClass)34.5 7.343e-03 1.676e-03 4.381 1.18e-05
## date2:as.factor(ageClass)44.5 7.737e-03 1.675e-03 4.618 3.87e-06
## date2:as.factor(ageClass)54.5 1.102e-02 1.691e-03 6.518 7.13e-11
## date2:as.factor(ageClass)64.5 1.100e-02 1.769e-03 6.220 4.97e-10
## date2:as.factor(ageClass)74.5 2.518e-02 1.923e-03 13.097 < 2e-16
## date2:as.factor(ageClass)84.5 2.475e-02 2.089e-03 11.846 < 2e-16
## date2:as.factor(ageClass)94.5 1.954e-02 2.628e-03 7.433 1.06e-13
##
## (Intercept) ***
## date2 ***
## as.factor(ageClass)14.5 ***
## as.factor(ageClass)24.5 ***
## as.factor(ageClass)34.5 ***
## as.factor(ageClass)44.5 ***
## as.factor(ageClass)54.5 ***
## as.factor(ageClass)64.5 ***
## as.factor(ageClass)74.5 ***
## as.factor(ageClass)84.5 ***
## as.factor(ageClass)94.5 ***
## reg_name.facBourgogne-Franche-Comté ***
## reg_name.facBretagne ***
## reg_name.facCentre-Val de Loire ***
## reg_name.facCorse ***
## reg_name.facGrand Est ***
## reg_name.facGuadeloupe ***
## reg_name.facGuyane ***
## reg_name.facHauts-de-France ***
## reg_name.facÃŽle-de-France ***
## reg_name.facLa Réunion ***
## reg_name.facMartinique ***
## reg_name.facMayotte ***
## reg_name.facNormandie ***
## reg_name.facNouvelle-Aquitaine
## reg_name.facOccitanie ***
## reg_name.facPays de la Loire ***
## reg_name.facProvence-Alpes-Côte d'Azur ***
## date2:as.factor(ageClass)14.5 ***
## date2:as.factor(ageClass)24.5 ***
## date2:as.factor(ageClass)34.5 ***
## date2:as.factor(ageClass)44.5 ***
## date2:as.factor(ageClass)54.5 ***
## date2:as.factor(ageClass)64.5 ***
## date2:as.factor(ageClass)74.5 ***
## date2:as.factor(ageClass)84.5 ***
## date2:as.factor(ageClass)94.5 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 113412.0 on 3049 degrees of freedom
## Residual deviance: 7502.1 on 3013 degrees of freedom
## (540 observations deleted due to missingness)
## AIC: 23559
##
## Number of Fisher Scoring iterations: 5
# Ignoring IND
mdl.narm <- glm(cbind(V1, notV1.narm) ~ date2 + cl_age90 + reg_name.fac, data = dat.regions.ages, family = "binomial")
summary(mdl.narm)
##
## Call:
## glm(formula = cbind(V1, notV1.narm) ~ date2 + cl_age90 + reg_name.fac,
## family = "binomial", data = dat.regions.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -7.787 -1.151 0.000 1.001 8.394
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.133e+03 6.223e+00 -182.136 < 2e-16
## date2 6.069e-02 3.331e-04 182.217 < 2e-16
## cl_age90 -7.529e-03 7.678e-05 -98.052 < 2e-16
## reg_name.facBourgogne-Franche-Comté -4.902e-01 9.795e-03 -50.044 < 2e-16
## reg_name.facBretagne 5.748e-01 1.091e-02 52.670 < 2e-16
## reg_name.facCentre-Val de Loire 2.077e-01 1.083e-02 19.180 < 2e-16
## reg_name.facCorse 1.604e+00 4.178e-02 38.396 < 2e-16
## reg_name.facGrand Est -4.678e-01 7.580e-03 -61.714 < 2e-16
## reg_name.facGuadeloupe 1.515e+00 7.173e-02 21.118 < 2e-16
## reg_name.facGuyane -3.838e-01 1.405e-01 -2.732 0.00629
## reg_name.facHauts-de-France 6.132e-01 6.489e-03 94.497 < 2e-16
## reg_name.facÃŽle-de-France 6.751e-01 5.985e-03 112.801 < 2e-16
## reg_name.facLa Réunion -2.693e+00 4.251e-02 -63.359 < 2e-16
## reg_name.facMartinique 4.591e-01 6.319e-02 7.264 3.75e-13
## reg_name.facMayotte -4.962e+00 2.049e-01 -24.220 < 2e-16
## reg_name.facNormandie 2.165e-01 9.468e-03 22.867 < 2e-16
## reg_name.facNouvelle-Aquitaine 2.485e-03 8.798e-03 0.282 0.77760
## reg_name.facOccitanie 3.609e-01 7.754e-03 46.546 < 2e-16
## reg_name.facPays de la Loire -5.727e-02 8.834e-03 -6.483 8.97e-11
## reg_name.facProvence-Alpes-Côte d'Azur 5.567e-01 6.873e-03 80.992 < 2e-16
##
## (Intercept) ***
## date2 ***
## cl_age90 ***
## reg_name.facBourgogne-Franche-Comté ***
## reg_name.facBretagne ***
## reg_name.facCentre-Val de Loire ***
## reg_name.facCorse ***
## reg_name.facGrand Est ***
## reg_name.facGuadeloupe ***
## reg_name.facGuyane **
## reg_name.facHauts-de-France ***
## reg_name.facÃŽle-de-France ***
## reg_name.facLa Réunion ***
## reg_name.facMartinique ***
## reg_name.facMayotte ***
## reg_name.facNormandie ***
## reg_name.facNouvelle-Aquitaine
## reg_name.facOccitanie ***
## reg_name.facPays de la Loire ***
## reg_name.facProvence-Alpes-Côte d'Azur ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 126975 on 3017 degrees of freedom
## Residual deviance: 10822 on 2998 degrees of freedom
## (540 observations deleted due to missingness)
## AIC: 26443
##
## Number of Fisher Scoring iterations: 5
par(mfrow = c(4, 3))
for(region in tmp){
subdat <- dat.regions[dat.regions$reg == region, ]
plot(subdat$date2, subdat$Prc_susp_501Y_V2_3, ylim = c(0, 100), main = regs[as.character(region)], col = colsAge[as.character(subdat$cl_age90)], pch = pchAge[as.character(subdat$cl_age90)],
xlab = "date", ylab = "Proportion V2/V3"
)
}
# Create new colums with information on number of specific PCR tests
# PCR with V2/3 result
dat.regions.ages$V23 <- dat.regions.ages$Nb_susp_501Y_V2_3
# All other PCRs (considering NAs are non-V1)
dat.regions.ages$notV23 <- dat.regions.ages$Nb_tests_PCR_TA_crible - dat.regions.ages$Nb_susp_501Y_V2_3
# All other PCRs with a result (removing NAs)
dat.regions.ages$notV23.narm <- dat.regions.ages$Nb_susp_501Y_V1 + dat.regions.ages$Nb_susp_ABS
# GLM
# Assuming that all IND (indetermine) are non-V23
mdl <- glm(cbind(V23, notV23) ~ date2 + ageClass + reg_name.fac, data = dat.regions.ages, family = "binomial")
summary(mdl)
##
## Call:
## glm(formula = cbind(V23, notV23) ~ date2 + ageClass + reg_name.fac,
## family = "binomial", data = dat.regions.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -6.9178 -0.8517 -0.2323 0.4906 5.6835
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.306e+02 1.318e+01 -9.909 < 2e-16
## date2 6.817e-03 7.052e-04 9.666 < 2e-16
## ageClass -2.886e-03 1.637e-04 -17.626 < 2e-16
## reg_name.facBourgogne-Franche-Comté 8.035e-02 2.455e-02 3.273 0.001063
## reg_name.facBretagne 3.729e-02 2.649e-02 1.408 0.159251
## reg_name.facCentre-Val de Loire -7.903e-01 3.736e-02 -21.153 < 2e-16
## reg_name.facCorse -2.181e+00 2.140e-01 -10.190 < 2e-16
## reg_name.facGrand Est 1.902e+00 1.415e-02 134.412 < 2e-16
## reg_name.facGuadeloupe -1.073e+00 2.254e-01 -4.760 1.94e-06
## reg_name.facGuyane -1.373e+01 1.936e+02 -0.071 0.943444
## reg_name.facHauts-de-France -4.878e-01 1.802e-02 -27.061 < 2e-16
## reg_name.facÃŽle-de-France 3.912e-01 1.418e-02 27.596 < 2e-16
## reg_name.facLa Réunion 2.913e+00 2.504e-02 116.350 < 2e-16
## reg_name.facMartinique -8.930e-01 2.446e-01 -3.650 0.000262
## reg_name.facMayotte 3.403e+00 3.476e-02 97.918 < 2e-16
## reg_name.facNormandie -1.351e-01 2.504e-02 -5.397 6.77e-08
## reg_name.facNouvelle-Aquitaine -1.305e-01 2.369e-02 -5.511 3.57e-08
## reg_name.facOccitanie -9.857e-01 2.731e-02 -36.095 < 2e-16
## reg_name.facPays de la Loire 5.875e-01 1.922e-02 30.561 < 2e-16
## reg_name.facProvence-Alpes-Côte d'Azur -1.747e-01 1.792e-02 -9.753 < 2e-16
##
## (Intercept) ***
## date2 ***
## ageClass ***
## reg_name.facBourgogne-Franche-Comté **
## reg_name.facBretagne
## reg_name.facCentre-Val de Loire ***
## reg_name.facCorse ***
## reg_name.facGrand Est ***
## reg_name.facGuadeloupe ***
## reg_name.facGuyane
## reg_name.facHauts-de-France ***
## reg_name.facÃŽle-de-France ***
## reg_name.facLa Réunion ***
## reg_name.facMartinique ***
## reg_name.facMayotte ***
## reg_name.facNormandie ***
## reg_name.facNouvelle-Aquitaine ***
## reg_name.facOccitanie ***
## reg_name.facPays de la Loire ***
## reg_name.facProvence-Alpes-Côte d'Azur ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 76763.8 on 3049 degrees of freedom
## Residual deviance: 5996.1 on 3030 degrees of freedom
## (540 observations deleted due to missingness)
## AIC: 16881
##
## Number of Fisher Scoring iterations: 15
# Ignoring IND
mdl.narm <- glm(cbind(V23, notV23.narm) ~ date2 + ageClass + reg_name.fac, data = dat.regions.ages, family = "binomial")
summary(mdl.narm)
##
## Call:
## glm(formula = cbind(V23, notV23.narm) ~ date2 + ageClass + reg_name.fac,
## family = "binomial", data = dat.regions.ages)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -7.2702 -0.8302 -0.2305 0.5206 5.6334
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.299e+02 1.328e+01 -9.779 < 2e-16
## date2 6.782e-03 7.107e-04 9.543 < 2e-16
## ageClass -2.845e-03 1.656e-04 -17.181 < 2e-16
## reg_name.facBourgogne-Franche-Comté 6.679e-02 2.457e-02 2.718 0.006565
## reg_name.facBretagne 2.638e-02 2.652e-02 0.995 0.319943
## reg_name.facCentre-Val de Loire -7.449e-01 3.740e-02 -19.920 < 2e-16
## reg_name.facCorse -2.092e+00 2.141e-01 -9.772 < 2e-16
## reg_name.facGrand Est 1.948e+00 1.420e-02 137.166 < 2e-16
## reg_name.facGuadeloupe -1.125e+00 2.254e-01 -4.991 6.01e-07
## reg_name.facGuyane -1.384e+01 2.127e+02 -0.065 0.948116
## reg_name.facHauts-de-France -4.677e-01 1.805e-02 -25.919 < 2e-16
## reg_name.facÃŽle-de-France 4.421e-01 1.420e-02 31.129 < 2e-16
## reg_name.facLa Réunion 3.165e+00 2.643e-02 119.751 < 2e-16
## reg_name.facMartinique -9.312e-01 2.447e-01 -3.806 0.000141
## reg_name.facMayotte 3.561e+00 3.665e-02 97.186 < 2e-16
## reg_name.facNormandie -1.015e-01 2.508e-02 -4.049 5.15e-05
## reg_name.facNouvelle-Aquitaine -1.296e-01 2.371e-02 -5.465 4.63e-08
## reg_name.facOccitanie -9.751e-01 2.733e-02 -35.683 < 2e-16
## reg_name.facPays de la Loire 5.833e-01 1.926e-02 30.291 < 2e-16
## reg_name.facProvence-Alpes-Côte d'Azur -1.509e-01 1.794e-02 -8.413 < 2e-16
##
## (Intercept) ***
## date2 ***
## ageClass ***
## reg_name.facBourgogne-Franche-Comté **
## reg_name.facBretagne
## reg_name.facCentre-Val de Loire ***
## reg_name.facCorse ***
## reg_name.facGrand Est ***
## reg_name.facGuadeloupe ***
## reg_name.facGuyane
## reg_name.facHauts-de-France ***
## reg_name.facÃŽle-de-France ***
## reg_name.facLa Réunion ***
## reg_name.facMartinique ***
## reg_name.facMayotte ***
## reg_name.facNormandie ***
## reg_name.facNouvelle-Aquitaine ***
## reg_name.facOccitanie ***
## reg_name.facPays de la Loire ***
## reg_name.facProvence-Alpes-Côte d'Azur ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 78608.9 on 3017 degrees of freedom
## Residual deviance: 5898.8 on 2998 degrees of freedom
## (540 observations deleted due to missingness)
## AIC: 16700
##
## Number of Fisher Scoring iterations: 15
par(mfrow = c(4, 3))
tmp <- unique(dat.regions$reg) # Region codes
tmp <- tmp[tmp>10 & tmp <= 93] # Choose only metropolitan regions
for(region in tmp){
subdat <- dat.regions[dat.regions$reg == region, ]
cc <- getVec(subdat[subdat$cl_age90 == 0, ], prop = FALSE)
plotDist(cc$x, cc$c1, cc$c23, cc$cABS, cc$cIND)
title(main = regs[as.character(region)])
}
URL <- "https://www.data.gouv.fr/fr/datasets/r/16f4fd03-797f-4616-bca9-78ff212d06e8"
dataFile <- paste0("data/Dep_", today, ".csv") # name file with today's date
download.file(URL, dataFile) # download file from repo
dat.deps <- read.csv(dataFile, sep = ";", stringsAsFactors = FALSE)
# Format date
dat.deps$date1 <- as.Date(substring(dat.deps$semaine, 1, 10))
dat.deps$date2 <- as.Date(substring(dat.deps$semaine, 12, 21))
# Rewrite time as days since beginning of the data
dat.deps$time <- dat.deps$date2 - min(dat.deps$date2)
# Compute data on total tests
dat.deps$Nb_tests_POS <- dat.deps$Nb_tests_PCR_TA_crible / (dat.deps$Prc_tests_PCR_TA_crible / 100)
# Add name
deps <- read.csv("data/departement2020.csv", stringsAsFactors = FALSE)
# Turn into dictionnary
dps <- deps$libelle
names(dps) <- as.character(deps$dep)
dat.deps$departement <- dps[as.character(dat.deps$dep)]
par(mfrow = c(35, 3))
for(idep in sort(unique(dat.deps$dep))){
tmp <- dat.deps[dat.deps$dep == idep, ]
plot(tmp$date2, tmp$Prc_susp_501Y_V1, ylim = c(0, 100), col = colsAge[as.character(tmp$cl_age90)], pch = pchAge[as.character(tmp$cl_age90)],
xlab = "date", ylab = "Proportion V1",
main = unique(tmp$departement))
# legend(x = min(dat.deps$date2), y = 100, legend = ages, pch = pchAge, col = colsAge)
}
par(mfrow = c(35, 3))
for(idep in sort(unique(dat.deps$dep))){
subdat <- dat.deps[dat.deps$dep == idep, ]
if(any(!is.na(subdat$Nb_tests_POS))){
cc <- getVec(subdat[subdat$cl_age90 == 0, ], prop = FALSE)
plotDist(cc$x, cc$c1, cc$c23, cc$cABS, cc$cIND)
title(main = unique(subdat$departement))
}
# legend(x = min(dat.deps$date2), y = 100, legend = ages, pch = pchAge, col = colsAge)
}